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Montero-Tena JA, Abdollahi Sisi N, Kox T, Abbadi A, Snowdon RJ, Golicz AA. haploMAGIC: accurate phasing and detection of recombination in multiparental populations despite genotyping errors. G3 (BETHESDA, MD.) 2024; 14:jkae109. [PMID: 38808682 DOI: 10.1093/g3journal/jkae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 02/12/2024] [Accepted: 05/08/2024] [Indexed: 05/30/2024]
Abstract
Recombination is a key mechanism in breeding for promoting genetic variability. Multiparental populations (MPPs) constitute an excellent platform for precise genotype phasing, identification of genome-wide crossovers (COs), estimation of recombination frequencies, and construction of recombination maps. Here, we introduce haploMAGIC, a pipeline to detect COs in MPPs with single-nucleotide polymorphism (SNP) data by exploiting the pedigree relationships for accurate genotype phasing and inference of grandparental haplotypes. haploMAGIC applies filtering to prevent false-positive COs due to genotyping errors (GEs), a common problem in high-throughput SNP analysis of complex plant genomes. Hence, it discards haploblocks not reaching a specified minimum number of informative alleles. A performance analysis using populations simulated with AlphaSimR revealed that haploMAGIC improves upon existing methods of CO detection in terms of recall and precision, most notably when GE rates are high. Furthermore, we constructed recombination maps using haploMAGIC with high-resolution genotype data from 2 large multiparental populations of winter rapeseed (Brassica napus). The results demonstrate the applicability of the pipeline in real-world scenarios and showed good correlations in recombination frequency compared with alternative software. Therefore, we propose haploMAGIC as an accurate tool at CO detection with MPPs that shows robustness against GEs.
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Affiliation(s)
- Jose A Montero-Tena
- Department of Agrobioinformatics, IFZ Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich Buff Ring 26, 35392 Giessen, Germany
| | - Nayyer Abdollahi Sisi
- Department of Plant Breeding, IFZ Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich Buff Ring 26, 35392 Giessen, Germany
| | - Tobias Kox
- NPZ Innovation GmbH, Hohenlieth-Hof, 24363 Holtsee, Germany
| | - Amine Abbadi
- NPZ Innovation GmbH, Hohenlieth-Hof, 24363 Holtsee, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich Buff Ring 26, 35392 Giessen, Germany
| | - Agnieszka A Golicz
- Department of Agrobioinformatics, IFZ Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich Buff Ring 26, 35392 Giessen, Germany
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Bilgrami S, Darzi Ramandi H, Farokhzadeh S, Rousseau-Gueutin M, Sobhani Najafabadi A, Ghaderian M, Huang P, Liu L. Meta-analysis of seed weight QTLome using a consensus and highly dense genetic map in Brassica napus L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:161. [PMID: 37354229 DOI: 10.1007/s00122-023-04401-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/02/2023] [Indexed: 06/26/2023]
Abstract
KEY MESSAGE We report here the discovery of high-confidence MQTL regions and of putative candidate genes associated with seed weight in B. napus using a highly dense consensus genetic map and by comparing various large-scale multiomics datasets. Seed weight (SW) is a direct determinant of seed yield in Brassica napus and is controlled by many loci. To unravel the main genomic regions associated with this complex trait, we used 13 available genetic maps to construct a consensus and highly dense map, comprising 40,401 polymorphic markers and 9191 genetic bins, harboring a cumulative length of 3047.8 cM. Then, we performed a meta-analysis using 639 projected SW quantitative trait loci (QTLs) obtained from studies conducted since 1999, enabling the identification of 57 meta-QTLS (MQTLs). The confidence intervals of our MQTLs were 9.8 and 4.3 times lower than the average CIs of the original QTLs for the A and C subgenomes, respectively, resulting in the detection of some key genes and several putative novel candidate genes associated with SW. By comparing the genes identified in MQTL intervals with multiomics datasets and coexpression analyses of common genes, we defined a more reliable and shorter list of putative candidate genes potentially involved in the regulation of seed maturation and SW. As an example, we provide a list of promising genes with high expression levels in seeds and embryos (e.g., BnaA03g04230D, BnaC03g08840D, BnaA10g29580D and BnaA03g27410D) that can be more finely studied through functional genetics experiments or that may be useful for MQTL-assisted breeding for SW. The high-density genetic consensus map and the single nucleotide polymorphism (SNP) physical map generated from the latest B. napus cv. Darmor-bzh v10 assembly will be a valuable resource for further mapping and map-based cloning of other important traits.
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Affiliation(s)
- Sayedehsaba Bilgrami
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Hadi Darzi Ramandi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
| | - Sara Farokhzadeh
- Department of Plant Production, College of Agriculture and Natural Resources of Darab, Shiraz University, Darab, Iran
| | | | - Ahmad Sobhani Najafabadi
- Department of Biotechnology, Agricultural Biotechnology Research Institute of Iran - Isfahan Branch, Agricultural Research, Education and Extension Organization (AREEO), Isfahan, Iran
| | - Mostafa Ghaderian
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA
| | - Pu Huang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China.
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Bhattarai G, Shi A, Mou B, Correll JC. Skim resequencing finely maps the downy mildew resistance loci RPF2 and RPF3 in spinach cultivars whale and Lazio. HORTICULTURE RESEARCH 2023; 10:uhad076. [PMID: 37323230 PMCID: PMC10261881 DOI: 10.1093/hr/uhad076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 04/10/2023] [Indexed: 06/17/2023]
Abstract
Commercial production of spinach (Spinacia oleracea L.) is centered in California and Arizona in the US, where downy mildew caused by Peronospora effusa is the most destructive disease. Nineteen typical races of P. effusa have been reported to infect spinach, with 16 identified after 1990. The regular appearance of new pathogen races breaks the resistance gene introgressed in spinach. We attempted to map and delineate the RPF2 locus at a finer resolution, identify linked single nucleotide polymorphism (SNP) markers, and report candidate downy mildew resistance (R) genes. Progeny populations segregating for RPF2 locus derived from resistant differential cultivar Lazio were infected using race 5 of P. effusa and were used to study for genetic transmission and mapping analysis in this study. Association analysis performed with low coverage whole genome resequencing-generated SNP markers mapped the RPF2 locus between 0.47 to 1.46 Mb of chromosome 3 with peak SNP (Chr3_1, 221, 009) showing a LOD value of 61.6 in the GLM model in TASSEL, which was within 1.08 Kb from Spo12821, a gene that encodes CC-NBS-LRR plant disease resistance protein. In addition, a combined analysis of progeny panels of Lazio and Whale segregating for RPF2 and RPF3 loci delineated the resistance section in chromosome 3 between 1.18-1.23 and 1.75-1.76 Mb. This study provides valuable information on the RPF2 resistance region in the spinach cultivar Lazio compared to RPF3 loci in the cultivar Whale. The RPF2 and RPF3 specific SNP markers, plus the resistant genes reported here, could add value to breeding efforts to develop downy mildew resistant cultivars in the future.
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Affiliation(s)
| | | | - Beiquan Mou
- USDA-ARS Crop Improvement and Protection Research Unit, Salinas, CA 93905, USA
| | - James C Correll
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701, USA
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Cai C, Pelé A, Bucher J, Finkers R, Bonnema G. Fine mapping of meiotic crossovers in Brassica oleracea reveals patterns and variations depending on direction and combination of crosses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:1192-1210. [PMID: 36626115 DOI: 10.1111/tpj.16104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
Meiotic recombination is crucial for assuring proper segregation of parental chromosomes and generation of novel allelic combinations. As this process is tightly regulated, identifying factors influencing rate, and distribution of meiotic crossovers (COs) is of major importance, notably for plant breeding programs. However, high-resolution recombination maps are sparse in most crops including the Brassica genus and knowledge about intraspecific variation and sex differences is lacking. Here, we report fine-scale resolution recombination landscapes for 10 female and 10 male crosses in Brassica oleracea, by analyzing progenies of five large four-way-cross populations from two reciprocally crossed F1s per population. Parents are highly diverse inbred lines representing major crops, including broccoli, cauliflower, cabbage, kohlrabi, and kale. We produced approximately 4.56T Illumina data from 1248 progenies and identified 15 353 CO across the 10 reciprocal crosses, 51.13% of which being mapped to <10 kb. We revealed fairly similar Mb-scale recombination landscapes among all cross combinations and between the sexes, and provided evidence that these landscapes are largely independent of sequence divergence. We evidenced strong influence of gene density and large structural variations on CO formation in B. oleracea. Moreover, we found extensive variations in CO number depending on the direction and combination of the initial parents crossed with, for the first time, a striking interdependency between these factors. These data improve our current knowledge on meiotic recombination and are important for Brassica breeders.
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Affiliation(s)
- Chengcheng Cai
- Plant Breeding, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Graduate School Experimental Plant Sciences, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Alexandre Pelé
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, 61-614, Poznan, Poland
| | - Johan Bucher
- Plant Breeding, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Richard Finkers
- Plant Breeding, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Gennovation B.V., Agro Business Park 10, 6708 PW, Wageningen, The Netherlands
| | - Guusje Bonnema
- Plant Breeding, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Graduate School Experimental Plant Sciences, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
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Abstract
Over the past decade, advances in plant genotyping have been critical in enabling the identification of genetic diversity, in understanding evolution, and in dissecting important traits in both crops and native plants. The widespread popularity of single-nucleotide polymorphisms (SNPs) has prompted significant improvements to SNP-based genotyping, including SNP arrays, genotyping by sequencing, and whole-genome resequencing. More recent approaches, including genotyping structural variants, utilizing pangenomes to capture species-wide genetic diversity and exploiting machine learning to analyze genotypic data sets, are pushing the boundaries of what plant genotyping can offer. In this chapter, we highlight these innovations and discuss how they will accelerate and advance future genotyping efforts.
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6
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Bhattarai G, Olaoye D, Mou B, Correll JC, Shi A. Mapping and selection of downy mildew resistance in spinach cv. whale by low coverage whole genome sequencing. FRONTIERS IN PLANT SCIENCE 2022; 13:1012923. [PMID: 36275584 PMCID: PMC9583407 DOI: 10.3389/fpls.2022.1012923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Spinach (Spinacia oleracea) is a popular leafy vegetable crop and commercial production is centered in California and Arizona in the US. The oomycete Peronospora effusa causes the most important disease in spinach, downy mildew. A total of nineteen races of P. effusa are known, with more than 15 documented in the last three decades, and the regular emergence of new races is continually overcoming the genetic resistance to the pathogen. This study aimed to finely map the downy mildew resistance locus RPF3 in spinach, identify single nucleotide polymorphism (SNP) markers associated with the resistance, refine the candidate genes responsible for the resistance, and evaluate the prediction performance using multiple machine learning genomic prediction (GP) methods. Segregating progeny population developed from a cross of resistant cultivar Whale and susceptible cultivar Viroflay to race 5 of P. effusa was inoculated under greenhouse conditions to determine downy mildew disease response across the panel. The progeny panel and the parents were resequenced at low coverage (1x) to identify genome wide SNP markers. Association analysis was performed using disease response phenotype data and SNP markers in TASSEL, GAPIT, and GENESIS programs and mapped the race 5 resistance loci (RPF3) to 1.25 and 2.73 Mb of Monoe-Viroflay chromosome 3 with the associated SNP in the 1.25 Mb region was 0.9 Kb from the NBS-LRR gene SOV3g001250. The RPF3 locus in the 1.22-1.23 Mb region of Sp75 chromosome 3 is 2.41-3.65 Kb from the gene Spo12821 annotated as NBS-LRR disease resistance protein. This study extended our understanding of the genetic basis of downy mildew resistance in spinach cultivar Whale and mapped the RPF3 resistance loci close to the NBS-LRR gene providing a target to pursue functional validation. Three SNP markers efficiently selected resistance based on multiple genomic selection (GS) models. The results from this study have added new genomic resources, generated an informed basis of the RPF3 locus resistant to spinach downy mildew pathogen, and developed markers and prediction methods to select resistant lines.
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Affiliation(s)
- Gehendra Bhattarai
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
| | - Dotun Olaoye
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
| | - Beiquan Mou
- Crop Improvement and Protection Research Unit, United States Department of Agriculture, Agricultural Research Service, Salinas, CA, United States
| | - James C. Correll
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR, United States
| | - Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
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Bayer PE, Gill M, Danilevicz MF, Edwards D. Producing High-Quality Single Nucleotide Polymorphism Data for Genome-Wide Association Studies. Methods Mol Biol 2022; 2481:153-159. [PMID: 35641763 DOI: 10.1007/978-1-0716-2237-7_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Single-nucleotide polymorphisms (SNPs) have become the primary type of molecular genetic marker used in a diverse range of genetic and genomic studies. SNPs can be used to identify genomic regions linked to traits such as disease in genome-wide association studies, to understand population structure and diversity, or to understand mechanisms of genome evolution. One of the first steps of any SNP-based workflow, following SNP discovery, is quality control of SNP data. The protocol described here details how to perform quality control on SNP data to minimise errors in downstream analysis.
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Affiliation(s)
- Philipp E Bayer
- Applied Bioinformatics Group, School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
| | - Mitchell Gill
- Applied Bioinformatics Group, School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
| | - Monica F Danilevicz
- Applied Bioinformatics Group, School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
| | - David Edwards
- Applied Bioinformatics Group, School of Biological Sciences, The University of Western Australia, Perth, WA, Australia.
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8
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Genomic regions associated with virulence in Setosphaeria turcica identified by linkage mapping in a biparental population. Fungal Genet Biol 2021; 159:103655. [PMID: 34954385 DOI: 10.1016/j.fgb.2021.103655] [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: 08/13/2021] [Revised: 11/17/2021] [Accepted: 12/19/2021] [Indexed: 01/06/2023]
Abstract
Northern corn leaf blight (NCLB) and sorghum leaf blight (SLB) are significant diseases of maize and sorghum, respectively, caused by the filamentous fungus Setosphaeria turcica. Strains of S. turcica are typically host-specific and infect either maize or sorghum. Host specificity in this pathogen is attributed to a single locus for maize and a second distinct locus for sorghum. To identify the genetic basis of host specificity in S. turcica, we generated a biparental population of S. turcica by crossing strains specific to maize and sorghum, phenotyped the population for leaf blight on sorghum and maize, genotyped the population to create a linkage map of S. turcica, and located candidate virulence regions. A total of 190 ascospores from 35 pseudothecia were isolated from the cross of maize and sorghum-specific strains. Greenhouse phenotyping of the biparental population (n = 144) showed independent inheritance of virulence, as indicated by a 1:1:1:1 segregation for virulence to maize, sorghum, both maize and sorghum, and avirulence to both crops. The population and host-specific parent strains were genotyped using genome skim sequencing on an Illumina NovaSeq 6000 platform resulting in over 780 million reads. A total of 32,635 variants including single nucleotide polymorphisms and indels were scored. There was evidence for a large deletion in the sorghum-specific strain of S. turcica. A genetic map consisting of 17 linkage groups spanning 3,069 centimorgans was constructed. Virulence to sorghum and maize mapped on distinct linkage groups with a significant QTL detected for virulence to maize. Furthermore, a single locus each for the in vitro traits hyphal growth rate and conidiation were identified and mapped onto two other linkage groups. In vitro traits did not correlate with in planta virulence complexity, suggesting that virulence on both hosts does not incur a fitness cost. Hyphal growth rate and conidiation were negatively correlated, indicating differences in hyphal growth versus dispersal ability for this pathogen. Identification of genetic regions underlying virulence specificity and saprotrophic growth traits in S. turcica provides a better understanding of the S. turcica- Andropogoneae pathosystem.
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Li G, Yue L, Cai X, Li F, Zhang H, Zhang S, Zhang S, Sun R. Fingerprint construction through genotyping by sequencing for applied breeding in Brassica rapa. Genome 2021; 65:105-113. [PMID: 34648727 DOI: 10.1139/gen-2021-0021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This study evaluated genotyping by sequencing (GBS) protocol for fingerprinting Brassica rapa and the data derived were more reliable than the re-sequencing data of B. rapa. Of the 10 enzyme solutions used to analyze the numbers of genotypes and single nucleotide polymorphisms (SNPs) in B. rapa, five solutions showed better results, namely: A (HaeIII, 450-500 bp), E (RsaI+HaeIII, 500-550 bp), F (RsaI+HaeIII, 500-600 bp), G (RsaI+HaeIII, 'All' fragment), and J (RsaI+EcoRV-HF®, 'All' fragment). The five enzyme solutions showed less than 40% similarity in different individuals from various samples, and 90% similarity in between two individuals from one sample. The E enzyme solution was most suitable for fingerprinting B. rapa revealing well-distributed SNPs in the whole genome. Of the 82 highly inbred lines and 18 F1 lines of B. rapa sequenced by GBS in E enzyme solution, known parents of 10 F1 lines were verified and male parents were discovered for 8 F1 lines that had only known female parents. This study provided a valuable method for screening parents for F1 lines in B. rapa for applied breeding through efficient evaluation of GBS with varied library construction strategies.
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Affiliation(s)
- Guoliang Li
- Chinese Academy of Agricultural Sciences, 12661, Haidian District, China;
| | - Lixin Yue
- CASS IVF, 471462, Beijing, Beijing, China;
| | - Xu Cai
- CASS IVF, 471462, Beijing, Beijing, China;
| | - Fei Li
- CASS IVF, 471462, Beijing, Beijing, China;
| | - Hui Zhang
- CASS IVF, 471462, Beijing, Beijing, China;
| | | | | | - Rifei Sun
- CASS IVF, 471462, Beijing, Beijing, China;
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QTL Genetic Mapping Study for Traits Affecting Meal Quality in Winter Oilseed Rape ( Brassica Napus L.). Genes (Basel) 2021; 12:genes12081235. [PMID: 34440409 PMCID: PMC8394057 DOI: 10.3390/genes12081235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/23/2021] [Accepted: 08/09/2021] [Indexed: 11/29/2022] Open
Abstract
Rapeseed (Brassica napus L.) meal is an important source of protein, but the presence of anti-nutritional compounds, such as fibre and glucosinolates, still limits its use as a livestock feed. Understanding the genetic basis of seed fibre biosynthesis would help to manipulate its content in seeds of oilseed rape. Here, we applied high-resolution skim genotyping by sequencing (SkimGBS) and characterised 187,835 single-nucleotide polymorphism (SNP) markers across a mapping population subsequently used for a genetic mapping study (R/qtl). This approach allowed the identification of 11 stable QTL related to seed quality traits and led to the identification of potential functional genes underlying these traits. Among these, key genes with a known role in carbohydrate metabolic process, cell wall, lignin, and flavonoid biosynthesis, including cellulase GH5, TT10/LAC15, TT4, and SUC2, were found. This study furthers the understanding of the molecular mechanisms underlying seed fibre content and provides new markers for molecular breeding in B. napus.
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Kumar P, Choudhary M, Jat BS, Kumar B, Singh V, Kumar V, Singla D, Rakshit S. Skim sequencing: an advanced NGS technology for crop improvement. J Genet 2021. [DOI: 10.1007/s12041-021-01285-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Skim-Sequencing Based Genotyping Reveals Genetic Divergence of the Wild and Domesticated Population of Black Tiger Shrimp ( Penaeus monodon) in the Indo-Pacific Region. BIOLOGY 2020; 9:biology9090277. [PMID: 32906759 PMCID: PMC7564732 DOI: 10.3390/biology9090277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/25/2020] [Accepted: 09/02/2020] [Indexed: 11/16/2022]
Abstract
The domestication of a wild-caught aquatic animal is an evolutionary process, which results in genetic discrimination at the genomic level in response to strong artificial selection. Although black tiger shrimp (Penaeus monodon) is one of the most commercially important aquaculture species, a systematic assessment of genetic divergence and structure of wild-caught and domesticated broodstock populations of the species is yet to be documented. Therefore, we used skim sequencing (SkimSeq) based genotyping approach to investigate the genetic structure of 50 broodstock individuals of P. monodon species, collected from five sampling sites (n = 10 in each site) across their distribution in Indo-Pacific regions. The wild-caught P. monodon broodstock population were collected from Malaysia (MS) and Japan (MJ), while domesticated broodstock populations were collected from Madagascar (MMD), Hawaii, HI, USA (MMO), and Thailand (MT). After various filtering process, a total of 194,259 single nucleotide polymorphism (SNP) loci were identified, in which 4983 SNP loci were identified as putatively adaptive by the pcadapt approach. In both datasets, pairwise FST estimates high genetic divergence between wild and domesticated broodstock populations. Consistently, different spatial clustering analyses in both datasets categorized divergent genetic structure into two clusters: (1) wild-caught populations (MS and MJ), and (2) domesticated populations (MMD, MMO and MT). Among 4983 putatively adaptive SNP loci, only 50 loci were observed to be in the coding region. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggested that non-synonymous mutated genes might be associated with the energy production, metabolic functions, respiration regulation and developmental rates, which likely act to promote adaptation to the strong artificial selection during the domestication process. This study has demonstrated the applicability of SkimSeq in a highly duplicated genome of P. monodon specifically, across a range of genetic backgrounds and geographical distributions, and would be useful for future genetic improvement program of this species in aquaculture.
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Xu Y, Liu X, Fu J, Wang H, Wang J, Huang C, Prasanna BM, Olsen MS, Wang G, Zhang A. Enhancing Genetic Gain through Genomic Selection: From Livestock to Plants. PLANT COMMUNICATIONS 2020; 1:100005. [PMID: 33404534 PMCID: PMC7747995 DOI: 10.1016/j.xplc.2019.100005] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Although long-term genetic gain has been achieved through increasing use of modern breeding methods and technologies, the rate of genetic gain needs to be accelerated to meet humanity's demand for agricultural products. In this regard, genomic selection (GS) has been considered most promising for genetic improvement of the complex traits controlled by many genes each with minor effects. Livestock scientists pioneered GS application largely due to livestock's significantly higher individual values and the greater reduction in generation interval that can be achieved in GS. Large-scale application of GS in plants can be achieved by refining field management to improve heritability estimation and prediction accuracy and developing optimum GS models with the consideration of genotype-by-environment interaction and non-additive effects, along with significant cost reduction. Moreover, it would be more effective to integrate GS with other breeding tools and platforms for accelerating the breeding process and thereby further enhancing genetic gain. In addition, establishing an open-source breeding network and developing transdisciplinary approaches would be essential in enhancing breeding efficiency for small- and medium-sized enterprises and agricultural research systems in developing countries. New strategies centered on GS for enhancing genetic gain need to be developed.
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Affiliation(s)
- Yunbi Xu
- Institute of Crop Science/CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- CIMMYT-China Tropical Maize Research Center, Foshan University, Foshan 528231, China
- CIMMYT-China Specialty Maize Research Center, Shanghai Academy of Agricultural Sciences, Shanghai 201400, China
| | - Xiaogang Liu
- Institute of Crop Science/CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Junjie Fu
- Institute of Crop Science/CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongwu Wang
- Institute of Crop Science/CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiankang Wang
- Institute of Crop Science/CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Changling Huang
- Institute of Crop Science/CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Boddupalli M. Prasanna
- CIMMYT (International Maize and Wheat Improvement Center), ICRAF Campus, United Nations Avenue, Nairobi, Kenya
| | - Michael S. Olsen
- CIMMYT (International Maize and Wheat Improvement Center), ICRAF Campus, United Nations Avenue, Nairobi, Kenya
| | - Guoying Wang
- Institute of Crop Science/CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Aimin Zhang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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14
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Genotyping-by-sequencing based QTL mapping for rice grain yield under reproductive stage drought stress tolerance. Sci Rep 2019; 9:14326. [PMID: 31586108 PMCID: PMC6778106 DOI: 10.1038/s41598-019-50880-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/12/2019] [Indexed: 12/27/2022] Open
Abstract
QTLs for rice grain yield under reproductive stage drought stress (qDTY) identified earlier with low density markers have shown linkage drag and need to be fine mapped before their utilization in breeding programs. In this study, genotyping-by-sequencing (GBS) based high-density linkage map of rice was developed using two BC1F3 mapping populations namely Swarna*2/Dular (3929 SNPs covering 1454.68 cM) and IR11N121*2/Aus196 (1191 SNPs covering 1399.68 cM) with average marker density of 0.37 cM to 1.18 cM respectively. In total, six qDTY QTLs including three consistent effect QTLs were identified in Swarna*2/Dular while eight qDTY QTLs including two consistent effect QTLs were identified in IR11N121*2/Aus 196 mapping population. Comparative analysis revealed four stable and novel QTLs (qDTY2.4, qDTY3.3, qDTY6.3, and qDTY11.2) which explained 8.62 to 14.92% PVE. However, one of the identified stable grain yield QTL qDTY1.1 in both the populations was located nearly at the same physical position of an earlier mapped major qDTY QTL. Further, the effect of the identified qDTY1.1 was validated in a subset of lines derived from five mapping populations confirming robustness of qDTY1.1 across various genetic backgrounds/seasons. The study successfully identified stable grain yield QTLs free from undesirable linkages of tall plant height/early maturity utilizing high density linkage maps.
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Tomkowiak A, Bocianowski J, Wolko Ł, Adamczyk J, Mikołajczyk S, Kowalczewski PŁ. Identification of Markers Associated with Yield Traits and Morphological Features in Maize ( Zea mays L.). PLANTS 2019; 8:plants8090330. [PMID: 31491958 PMCID: PMC6783969 DOI: 10.3390/plants8090330] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 08/30/2019] [Accepted: 09/03/2019] [Indexed: 12/05/2022]
Abstract
Association mapping is a powerful approach to detect associations between traits of interest and genetic markers based on linkage disequilibrium in molecular plant breeding. The aim of this study was the identification of single nucleotide polymorphisms (SNPs) and SilicoDArT markers associated with yield traits and morphological features in maize. Plant material constituted inbred lines. The field experiment with inbred lines was established on 10 m2 plots in a set of complete random blocks in three replicates. We observed 22 quantitative traits. Association mapping was performed in this study using a method based on the mixed linear model with the population structure estimated by eigenanalysis (principal component analysis applied to all markers) and modeled by random effects. As a result of mapping, 969 markers (346 SNPs and 623 SilocoDArT) were selected from 49,911 identified polymorphic molecular markers, which were significantly associated with the analyzed morphological features and yield structure traits. Markers associated with five or six traits were selected during further analyses, including SilicoDArT 4591115 (anthocyanin coloration of anthers, length of main axis above the highest lateral branch, cob length, number of grains per cob, weight of fresh grains per cob and weight of fresh grains per cob at 15% moisture), SilicoDArT 7059939 (anthocyanin coloration of glumes of cob, time of anthesis—50% of flowering plants, time of silk emergence—50% of flowering plants, anthocyanin coloration of anthers and cob diameter), SilicoDArT 5587991 (anthocyanin coloration of glumes of cob, time of anthesis—50% of flowering plants, anthocyanin coloration of anthers, curvature of lateral branches and number of rows of grain). The two genetic similarity dendrograms between the inbred lines were constructed based on all significant SNPs and SilicoDArT markers. On both dendrograms lines clustered according to the kernel structure (flint, dent) and origin. The selected markers may be useful in predicting hybrid formulas in a heterosis culture. The present study demonstrated that molecular SNP and Silico DArT markers could be used in this species to group lines in terms of origin and lines with incomplete origin data. They can also be useful in maize in predicting the hybrid formula and can find applications in the selection of parental components for heterosis crossings.
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Affiliation(s)
- Agnieszka Tomkowiak
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, 11 Dojazd St., 60-632 Poznań, Poland.
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, 28 Wojska Polskiego St., 60-637 Poznań, Poland.
| | - Łukasz Wolko
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, 11 Dojazd St., 60-632 Poznań, Poland.
| | - Józef Adamczyk
- Plant Breeding Smolice Ltd., Co., Smolice 146, 63-740 Kobylin, Poland.
| | - Sylwia Mikołajczyk
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, 11 Dojazd St., 60-632 Poznań, Poland.
| | - Przemysław Łukasz Kowalczewski
- Institute of Food Technology of Plant Origin, Poznań University of Life Sciences, 31 Wojska Polskiego St., 60-624 Poznań, Poland.
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16
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Kreplak J, Madoui MA, Cápal P, Novák P, Labadie K, Aubert G, Bayer PE, Gali KK, Syme RA, Main D, Klein A, Bérard A, Vrbová I, Fournier C, d'Agata L, Belser C, Berrabah W, Toegelová H, Milec Z, Vrána J, Lee H, Kougbeadjo A, Térézol M, Huneau C, Turo CJ, Mohellibi N, Neumann P, Falque M, Gallardo K, McGee R, Tar'an B, Bendahmane A, Aury JM, Batley J, Le Paslier MC, Ellis N, Warkentin TD, Coyne CJ, Salse J, Edwards D, Lichtenzveig J, Macas J, Doležel J, Wincker P, Burstin J. A reference genome for pea provides insight into legume genome evolution. Nat Genet 2019; 51:1411-1422. [PMID: 31477930 DOI: 10.1038/s41588-019-0480-1] [Citation(s) in RCA: 238] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 07/10/2019] [Indexed: 02/03/2023]
Abstract
We report the first annotated chromosome-level reference genome assembly for pea, Gregor Mendel's original genetic model. Phylogenetics and paleogenomics show genomic rearrangements across legumes and suggest a major role for repetitive elements in pea genome evolution. Compared to other sequenced Leguminosae genomes, the pea genome shows intense gene dynamics, most likely associated with genome size expansion when the Fabeae diverged from its sister tribes. During Pisum evolution, translocation and transposition differentially occurred across lineages. This reference sequence will accelerate our understanding of the molecular basis of agronomically important traits and support crop improvement.
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Affiliation(s)
- Jonathan Kreplak
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Mohammed-Amin Madoui
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Petr Cápal
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Petr Novák
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Grégoire Aubert
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia
| | - Krishna K Gali
- Crop Development Centre/Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Robert A Syme
- Centre for Crop and Disease Management, Curtin University, Bentley, Western Australia, Australia
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Anthony Klein
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Aurélie Bérard
- Etude du Polymorphisme des Génomes Végétaux, INRA, Université Paris-Saclay, Evry, France
| | - Iva Vrbová
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Cyril Fournier
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Leo d'Agata
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Caroline Belser
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Wahiba Berrabah
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Helena Toegelová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Zbyněk Milec
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - HueyTyng Lee
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Ayité Kougbeadjo
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Morgane Térézol
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Cécile Huneau
- UMR 1095 Génétique, Diversité, Ecophysiologie des Céréales, INRA, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Chala J Turo
- Centre for Crop and Disease Management, School of Molecular and Life Science, Curtin University, Bentley, Western Australia, Australia
| | | | - Pavel Neumann
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Matthieu Falque
- GQE-Le Moulon, INRA, University of Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Karine Gallardo
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté Bourgogne, Université Bourgogne Franche-Comté, Dijon, France
| | - Rebecca McGee
- USDA Agricultural Research Service, Pullman, WA, USA
| | - Bunyamin Tar'an
- Crop Development Centre/Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay, INRA, CNRS, University of Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Orsay, France
| | - Jean-Marc Aury
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia
| | | | - Noel Ellis
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Thomas D Warkentin
- Crop Development Centre/Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | | | - Jérome Salse
- UMR 1095 Génétique, Diversité, Ecophysiologie des Céréales, INRA, Université Clermont Auvergne, Clermont-Ferrand, France
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia
| | - Judith Lichtenzveig
- School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Jiří Macas
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Judith Burstin
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne Franche-Comté Bourgogne, Université Bourgogne Franche-Comté, Dijon, France.
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Happ MM, Wang H, Graef GL, Hyten DL. Generating High Density, Low Cost Genotype Data in Soybean [ Glycine max (L.) Merr.]. G3 (BETHESDA, MD.) 2019; 9:2153-2160. [PMID: 31072870 PMCID: PMC6643887 DOI: 10.1534/g3.119.400093] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/01/2019] [Indexed: 11/18/2022]
Abstract
Obtaining genome-wide genotype information for millions of SNPs in soybean [Glycine max (L.) Merr.] often involves completely resequencing a line at 5X or greater coverage. Currently, hundreds of soybean lines have been resequenced at high depth levels with their data deposited in the NCBI Short Read Archive. This publicly available dataset may be leveraged as an imputation reference panel in combination with skim (low coverage) sequencing of new soybean genotypes to economically obtain high-density SNP information. Ninety-nine soybean lines resequenced at an average of 17.1X were used to generate a reference panel, with over 10 million SNPs called using GATK's Haplotype Caller tool. Whole genome resequencing at approximately 1X depth was performed on 114 previously ungenotyped experimental soybean lines. Coverages down to 0.1X were analyzed by randomly subsetting raw reads from the original 1X sequence data. SNPs discovered in the reference panel were genotyped in the experimental lines after aligning to the soybean reference genome, and missing markers imputed using Beagle 4.1. Sequencing depth of the experimental lines could be reduced to 0.3X while still retaining an accuracy of 97.8%. Accuracy was inversely related to minor allele frequency, and highly correlated with marker linkage disequilibrium. The high accuracy of skim sequencing combined with imputation provides a low cost method for obtaining dense genotypic information that can be used for various genomics applications in soybean.
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Affiliation(s)
- Mary M Happ
- University of Nebraska-Lincoln, Lincoln, NE 68503
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18
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Mirzaghaderi G, Mason AS. Broadening the bread wheat D genome. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1295-1307. [PMID: 30739154 DOI: 10.1007/s00122-019-03299-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 02/02/2019] [Indexed: 05/21/2023]
Abstract
Although Ae. tauschii has been extensively utilised for wheat breeding, the D-genome-containing allopolyploids have largely remained unexploited. In this review, we discuss approaches that can be used to exploit the D genomes of the different Aegilops species for the improvement of bread wheat. The D genome of allohexaploid bread wheat (Triticum aestivum, 2n = AABBDD) is the least diverse of the three wheat genomes and is unarguably less diverse than that of diploid progenitor Aegilops tauschii (2n = DD). Useful genetic variation and phenotypic traits also exist within each of the wheat group species containing a copy of the D genome: allopolyploid Aegilops species Ae. cylindrica (2n = DcDcCcCc), Ae. crassa 4x (2n = D1D1XcrXcr), Ae. crassa 6x (2n = D1D1XcrXcrDcrDcr), Ae. ventricosa (2n = DvDvNvNv), Ae. vavilovii (2n = D1D1XcrXcrSvSv) and Ae. juvenalis (2n = D1D1XcrXcrUjUj). Although Ae. tauschii has been extensively utilised for wheat breeding, the D-genome-containing allopolyploids have largely remained unexploited. Some of these D genomes appear to be modified relative to the bread wheat and Ae. tauschii D genomes, and others present in the allopolyploids may also contain useful variation as a result of adaptation to an allopolyploid, multi-genome environment. We summarise the genetic relationships, karyotypic variation and phenotypic traits known to be present in each of the D genome species that could be of relevance for bread wheat improvement and discuss approaches that can be used to exploit the D genomes of the different Aegilops species for the improvement of bread wheat. Better understanding of factors controlling chromosome inheritance and recombination in wheat group interspecific hybrids, as well as effective utilisation of new and developing genetics and genomics technologies, have great potential to improve the agronomic potential of the bread wheat D genome.
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Affiliation(s)
- Ghader Mirzaghaderi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, P. O. Box 416, Sanandaj, Iran.
| | - Annaliese S Mason
- Department of Plant Breeding, Justus Liebig University, IFZ Research Centre for Biosystems, Land Use and Nutrition, Heinrich-Buff-Ring 26-32, Giessen, 35392, Germany
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19
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Scheben A, Verpaalen B, Lawley CT, Chan CKK, Bayer PE, Batley J, Edwards D. CropSNPdb: a database of SNP array data for Brassica crops and hexaploid bread wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:142-152. [PMID: 30548723 DOI: 10.1111/tpj.14194] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 05/23/2023]
Abstract
Advances in sequencing technology have led to a rapid rise in the genomic data available for plants, driving new insights into the evolution, domestication and improvement of crops. Single nucleotide polymorphisms (SNPs) are a major component of crop genomic diversity, and are invaluable as genetic markers in research and breeding programs. High-throughput SNP arrays, or 'SNP chips', can generate reproducible sets of informative SNP markers and have been broadly adopted. Although there are many public repositories for sequencing data, which are routinely uploaded, there are no formal repositories for crop SNP array data. To make SNP array data more easily accessible, we have developed CropSNPdb (http://snpdb.appliedbioinformatics.com.au), a database for SNP array data produced by the Illumina Infinium™ hexaploid bread wheat (Triticum aestivum) 90K and Brassica 60K arrays. We currently host SNPs from datasets covering 526 Brassica lines and 309 bread wheat lines, and provide search, download and upload utilities for users. CropSNPdb provides a useful repository for these data, which can be applied for a range of genomics and molecular crop-breeding activities.
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Affiliation(s)
- Armin Scheben
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Brent Verpaalen
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | | | - Chon-Kit K Chan
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
- Australian Genome Research Facility, Melbourne, Vic., 3000, Australia
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
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20
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Voss-Fels KP, Cooper M, Hayes BJ. Accelerating crop genetic gains with genomic selection. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:669-686. [PMID: 30569365 DOI: 10.1007/s00122-018-3270-8] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 12/12/2018] [Indexed: 05/05/2023]
Abstract
Genomic prediction based on additive genetic effects can accelerate genetic gain. There are opportunities for further improvement by including non-additive effects that access untapped sources of genetic diversity. Several studies have reported a worrying gap between the projected global future demand for plant-based products and the current annual rates of production increase, indicating that enhancing the rate of genetic gain might be critical for future food security. Therefore, new breeding technologies and strategies are required to significantly boost genetic improvement of future crop cultivars. Genomic selection (GS) has delivered considerable genetic gain in animal breeding and is becoming an essential component of many modern plant breeding programmes as well. In this paper, we review the lessons learned from implementing GS in livestock and the impact of GS on crop breeding, and discuss important features for the success of GS under different breeding scenarios. We highlight major challenges associated with GS including rapid genotyping, phenotyping, genotype-by-environment interaction and non-additivity and give examples for opportunities to overcome these issues. Finally, the potential of combining GS with other modern technologies in order to maximise the rate of crop genetic improvement is discussed, including the potential of increasing prediction accuracy by integration of crop growth models in GS frameworks.
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Affiliation(s)
- Kai Peter Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Mark Cooper
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Ben John Hayes
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia.
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21
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Nguyen KL, Grondin A, Courtois B, Gantet P. Next-Generation Sequencing Accelerates Crop Gene Discovery. TRENDS IN PLANT SCIENCE 2019; 24:263-274. [PMID: 30573308 DOI: 10.1016/j.tplants.2018.11.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/20/2018] [Accepted: 11/22/2018] [Indexed: 05/22/2023]
Abstract
The identification and isolation of genes underlying quantitative trait loci (QTLs) associated with agronomic traits in crops have been recently accelerated thanks to next-generation sequencing (NGS)-based technologies combined with plant genetics. With NGS, various revisited genetic approaches, which benefited from higher marker density, have been elaborated. These approaches improved resolution in QTL position and assisted in determining functional causative variations in genes. Examples of QTLs/genes associated with agronomic traits in crops and identified using different strategies based on whole-genome sequencing (WGS)/whole-genome resequencing (WGR) or RNA-seq are presented and discussed in this review. More specifically, we summarize and illustrate how NGS boosted bulk-segregant analysis (BSA), expression profiling, and the construction of polymorphism databases to facilitate the detection of QTLs and causative genes.
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Affiliation(s)
- Khanh Le Nguyen
- Université de Montpellier, Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier cedex 5, France; LMI RICE 2, AGI, Km2 Pham Van Dong, Tu Liem, Hanoi, Vietnam
| | - Alexandre Grondin
- Université de Montpellier, Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier cedex 5, France
| | - Brigitte Courtois
- CIRAD, UMR AGAP, F-34398 Montpellier, France; Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Pascal Gantet
- Université de Montpellier, Institut de Recherche pour le Développement, UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier cedex 5, France; Centre of the Region Haná for Biotechnological and Agricultural Research, Dept. of Molecular Biology, Faculty of Science, Palacký University, Olomouc, Czech Republic.
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22
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Malmberg MM, Barbulescu DM, Drayton MC, Shinozuka M, Thakur P, Ogaji YO, Spangenberg GC, Daetwyler HD, Cogan NOI. Evaluation and Recommendations for Routine Genotyping Using Skim Whole Genome Re-sequencing in Canola. FRONTIERS IN PLANT SCIENCE 2018; 9:1809. [PMID: 30581450 PMCID: PMC6292936 DOI: 10.3389/fpls.2018.01809] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/21/2018] [Indexed: 05/25/2023]
Abstract
Whole genome sequencing offers genome wide, unbiased markers, and inexpensive library preparation. With the cost of sequencing decreasing rapidly, many plant genomes of modest size are amenable to skim whole genome resequencing (skim WGR). The use of skim WGR in diverse sample sets without the use of imputation was evaluated in silico in 149 canola samples representative of global diversity. Fastq files with an average of 10x coverage of the reference genome were used to generate skim samples representing 0.25x, 0.5x, 1x, 2x, 3x, 4x, and 5x sequencing coverage. Applying a pre-defined list of SNPs versus de novo SNP discovery was evaluated. As skim WGR is expected to result in some degree of insufficient allele sampling, all skim coverage levels were filtered at a range of minimum read depths from a relaxed minimum read depth of 2 to a stringent read depth of 5, resulting in 28 list-based SNP sets. As a broad recommendation, genotyping pre-defined SNPs between 1x and 2x coverage with relatively stringent depth filtering is appropriate for a diverse sample set of canola due to a balance between marker number, sufficient accuracy, and sequencing cost, but depends on the intended application. This was experimentally examined in two sample sets with different genetic backgrounds: 1x coverage of 1,590 individuals from 84 Australian spring type four-parent crosses aimed at maximizing diversity as well as one commercial F1 hybrid, and 2x coverage of 379 doubled haploids (DHs) derived from a subset of the four-parent crosses. To determine optimal coverage in a simpler genetic background, the DH sample sequence coverage was further down sampled in silico. The flexible and cost-effective nature of the protocol makes it highly applicable across a range of species and purposes.
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Affiliation(s)
- M. Michelle Malmberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | | | - Michelle C. Drayton
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Maiko Shinozuka
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Preeti Thakur
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Yvonne O. Ogaji
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - German C. Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Hans D. Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Noel O. I. Cogan
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
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Malmberg MM, Shi F, Spangenberg GC, Daetwyler HD, Cogan NOI. Diversity and Genome Analysis of Australian and Global Oilseed Brassica napus L. Germplasm Using Transcriptomics and Whole Genome Re-sequencing. FRONTIERS IN PLANT SCIENCE 2018; 9:508. [PMID: 29725344 PMCID: PMC5917405 DOI: 10.3389/fpls.2018.00508] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/03/2018] [Indexed: 05/21/2023]
Abstract
Intensive breeding of Brassica napus has resulted in relatively low diversity, such that B. napus would benefit from germplasm improvement schemes that sustain diversity. As such, samples representative of global germplasm pools need to be assessed for existing population structure, diversity and linkage disequilibrium (LD). Complexity reduction genotyping-by-sequencing (GBS) methods, including GBS-transcriptomics (GBS-t), enable cost-effective screening of a large number of samples, while whole genome re-sequencing (WGR) delivers the ability to generate large numbers of unbiased genomic single nucleotide polymorphisms (SNPs), and identify structural variants (SVs). Furthermore, the development of genomic tools based on whole genomes representative of global oilseed diversity and orientated by the reference genome has substantial industry relevance and will be highly beneficial for canola breeding. As recent studies have focused on European and Chinese varieties, a global diversity panel as well as a substantial number of Australian spring types were included in this study. Focusing on industry relevance, 633 varieties were initially genotyped using GBS-t to examine population structure using 61,037 SNPs. Subsequently, 149 samples representative of global diversity were selected for WGR and both data sets used for a side-by-side evaluation of diversity and LD. The WGR data was further used to develop genomic resources consisting of a list of 4,029,750 high-confidence SNPs annotated using SnpEff, and SVs in the form of 10,976 deletions and 2,556 insertions. These resources form the basis of a reliable and repeatable system allowing greater integration between canola genomics studies, with a strong focus on breeding germplasm and industry applicability.
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Affiliation(s)
- M. Michelle Malmberg
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Fan Shi
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia
| | - German C. Spangenberg
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Hans D. Daetwyler
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Noel O. I. Cogan
- AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
- *Correspondence: Noel O. I. Cogan,
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Scheben A, Batley J, Edwards D. Revolution in Genotyping Platforms for Crop Improvement. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 164:37-52. [PMID: 29356847 DOI: 10.1007/10_2017_47] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the past decade, the application of high-throughput sequencing to crop genotyping has given rise to novel platforms capable of genotyping tens of thousands of genome-wide DNA markers. Coupled with the decreasing costs of sequencing, this rapid increase in markers allows accelerated and highly accurate genotyping of entire crop populations and diversity sets using single nucleotide polymorphisms (SNPs). These revolutionary advances accelerate crop improvement by facilitating a more precise connection of phenotype to genotype through association studies, linkage mapping and diversity analysis. The platforms driving the advances in genotyping are array technologies and genotyping by sequencing (GBS) methods, which include both low-coverage whole genome resequencing (skim sequencing) and reduced representation sequencing (RRS) approaches. Here, we outline and compare these genotyping platforms and provide a perspective on the promising future of crop genotyping. While SNP arrays provide high quality, simple handling, and unchallenging analysis, the lower cost of RRS and the greater data volume produced by skim sequencing suggest that use of GBS will become more prevalent in crop genomics as sequencing costs decrease and data analysis becomes more streamlined. Graphical Abstract.
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Affiliation(s)
- Armin Scheben
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia.,Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia. .,Institute of Agriculture, University of Western Australia, Crawley, WA, Australia.
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Gacek K, Bartkowiak-Broda I, Batley J. Genetic and Molecular Regulation of Seed Storage Proteins (SSPs) to Improve Protein Nutritional Value of Oilseed Rape ( Brassica napus L.) Seeds. FRONTIERS IN PLANT SCIENCE 2018; 9:890. [PMID: 30013586 PMCID: PMC6036235 DOI: 10.3389/fpls.2018.00890] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/07/2018] [Indexed: 05/20/2023]
Abstract
The world-wide demand for additional protein sources for human nutrition and animal feed keeps rising due to rapidly growing world population. Oilseed rape is a second important oil producing crop and the by-product of the oil production is a protein rich meal. The protein in rapeseed meal finds its application in animal feed and various industrial purposes, but its improvement is of great interest, especially for non-ruminants and poultry feed. To be able to manipulate the quality and quantity of seed protein in oilseed rape, understanding genetic architecture of seed storage protein (SSPs) synthesis and accumulation in this crop species is of great interest. For this, application of modern molecular breeding tools such as whole genome sequencing, genotyping, association mapping, and genome editing methods implemented in oilseed rape seed protein improvement would be of great interest. This review examines current knowledge and opportunities to manipulate of SSPs in oilseed rape to improve its quality, quantity and digestibility.
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Affiliation(s)
- Katarzyna Gacek
- Oilseed Crops Research Centre, Plant Breeding and Acclimatization Institute-National Research Institute, Poznań, Poland
| | - Iwona Bartkowiak-Broda
- Oilseed Crops Research Centre, Plant Breeding and Acclimatization Institute-National Research Institute, Poznań, Poland
| | - Jacqueline Batley
- School of Biological Sciences, The University of Western Australia, Crawley, WA, Australia
- *Correspondence: Jacqueline Batley,
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Dolatabadian A, Patel DA, Edwards D, Batley J. Copy number variation and disease resistance in plants. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:2479-2490. [PMID: 29043379 DOI: 10.1007/s00122-017-2993-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 09/27/2017] [Indexed: 05/06/2023]
Abstract
Plant genome diversity varies from single nucleotide polymorphisms to large-scale deletions, insertions, duplications, or re-arrangements. These re-arrangements of sequences resulting from duplication, gains or losses of DNA segments are termed copy number variations (CNVs). During the last decade, numerous studies have emphasized the importance of CNVs as a factor affecting human phenotype; in particular, CNVs have been associated with risks for several severe diseases. In plants, the exploration of the extent and role of CNVs in resistance against pathogens and pests is just beginning. Since CNVs are likely to be associated with disease resistance in plants, an understanding of the distribution of CNVs could assist in the identification of novel plant disease-resistance genes. In this paper, we review existing information about CNVs; their importance, role and function, as well as their association with disease resistance in plants.
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Affiliation(s)
- Aria Dolatabadian
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia
| | - Dhwani Apurva Patel
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, WA, 6009, Australia.
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Bayer PE, Hurgobin B, Golicz AA, Chan CK, Yuan Y, Lee H, Renton M, Meng J, Li R, Long Y, Zou J, Bancroft I, Chalhoub B, King GJ, Batley J, Edwards D. Assembly and comparison of two closely related Brassica napus genomes. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1602-1610. [PMID: 28403535 PMCID: PMC5698052 DOI: 10.1111/pbi.12742] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 02/06/2017] [Accepted: 04/09/2017] [Indexed: 05/18/2023]
Abstract
As an increasing number of plant genome sequences become available, it is clear that gene content varies between individuals, and the challenge arises to predict the gene content of a species. However, genome comparison is often confounded by variation in assembly and annotation. Differentiating between true gene absence and variation in assembly or annotation is essential for the accurate identification of conserved and variable genes in a species. Here, we present the de novo assembly of the B. napus cultivar Tapidor and comparison with an improved assembly of the Brassica napus cultivar Darmor-bzh. Both cultivars were annotated using the same method to allow comparison of gene content. We identified genes unique to each cultivar and differentiate these from artefacts due to variation in the assembly and annotation. We demonstrate that using a common annotation pipeline can result in different gene predictions, even for closely related cultivars, and repeat regions which collapse during assembly impact whole genome comparison. After accounting for differences in assembly and annotation, we demonstrate that the genome of Darmor-bzh contains a greater number of genes than the genome of Tapidor. Our results are the first step towards comparison of the true differences between B. napus genomes and highlight the potential sources of error in future production of a B. napus pangenome.
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Affiliation(s)
- Philipp E. Bayer
- School of Biological SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - Bhavna Hurgobin
- School of Biological SciencesThe University of Western AustraliaCrawleyWAAustralia
- School of Agriculture and Food SciencesUniversity of QueenslandSt. LuciaQldAustralia
| | - Agnieszka A. Golicz
- Plant Molecular Biology and Biotechnology LaboratoryFaculty of Veterinary and Agricultural SciencesUniversity of Melbourne, ParkvilleMelbourneVic.Australia
| | | | - Yuxuan Yuan
- School of Biological SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - HueyTyng Lee
- School of Biological SciencesThe University of Western AustraliaCrawleyWAAustralia
- School of Agriculture and Food SciencesUniversity of QueenslandSt. LuciaQldAustralia
| | - Michael Renton
- School of Biological SciencesThe University of Western AustraliaCrawleyWAAustralia
- School of Agriculture and EnvironmentThe University of Western AustraliaCrawleyWAAustralia
| | - Jinling Meng
- National Key Laboratory of Crop Genetic ImprovementKey Laboratory of Rapeseed Genetic ImprovementMinistry of Agriculture P. R. ChinaHuazhong Agricultural UniversityWuhanChina
| | - Ruiyuan Li
- National Key Laboratory of Crop Genetic ImprovementKey Laboratory of Rapeseed Genetic ImprovementMinistry of Agriculture P. R. ChinaHuazhong Agricultural UniversityWuhanChina
| | - Yan Long
- National Key Laboratory of Crop Genetic ImprovementKey Laboratory of Rapeseed Genetic ImprovementMinistry of Agriculture P. R. ChinaHuazhong Agricultural UniversityWuhanChina
| | - Jun Zou
- National Key Laboratory of Crop Genetic ImprovementKey Laboratory of Rapeseed Genetic ImprovementMinistry of Agriculture P. R. ChinaHuazhong Agricultural UniversityWuhanChina
| | | | - Boulos Chalhoub
- Organization and Evolution of Complex Genomes (OECG)Institut National de la Recherche agronomique (INRA)Université d'Evry Val d'Essonne (UEVE)EvryFrance
- Institute of System and Synthetic Biology, GenopoleCentre National de la Recherche ScientifiqueUniversité d'Evry Val d'EssonneUniversité Paris‐SaclayEvryFrance
| | - Graham J. King
- National Key Laboratory of Crop Genetic ImprovementKey Laboratory of Rapeseed Genetic ImprovementMinistry of Agriculture P. R. ChinaHuazhong Agricultural UniversityWuhanChina
- Southern Cross Plant ScienceSouthern Cross UniversityLismoreNSWAustralia
| | - Jacqueline Batley
- School of Biological SciencesThe University of Western AustraliaCrawleyWAAustralia
| | - David Edwards
- School of Biological SciencesThe University of Western AustraliaCrawleyWAAustralia
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Neik TX, Barbetti MJ, Batley J. Current Status and Challenges in Identifying Disease Resistance Genes in Brassica napus. FRONTIERS IN PLANT SCIENCE 2017; 8:1788. [PMID: 29163558 PMCID: PMC5681527 DOI: 10.3389/fpls.2017.01788] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 10/02/2017] [Indexed: 05/18/2023]
Abstract
Brassica napus is an economically important crop across different continents including temperate and subtropical regions in Europe, Canada, South Asia, China and Australia. Its widespread cultivation also brings setbacks as it plays host to fungal, oomycete and chytrid pathogens that can lead to serious yield loss. For sustainable crop production, identification of resistance (R) genes in B. napus has become of critical importance. In this review, we discuss four key pathogens affecting Brassica crops: Clubroot (Plasmodiophora brassicae), Blackleg (Leptosphaeria maculans and L. biglobosa), Sclerotinia Stem Rot (Sclerotinia sclerotiorum), and Downy Mildew (Hyaloperonospora parasitica). We first review current studies covering prevalence of these pathogens on Brassica crops and highlight the R genes and QTL that have been identified from Brassica species against these pathogens. Insights into the relationships between the pathogen and its Brassica host, the unique host resistance mechanisms and how these affect resistance outcomes is also presented. We discuss challenges in identification and deployment of R genes in B. napus in relation to highly specific genetic interactions between host subpopulations and pathogen pathotypes and emphasize the need for common or shared techniques and research materials or tighter collaboration between researchers to reconcile the inconsistencies in the research outcomes. Using current genomics tools, we provide examples of how characterization and cloning of R genes in B. napus can be carried out more effectively. Lastly, we put forward strategies to breed resistant cultivars through introgressions supported by genomic approaches and suggest prospects that can be implemented in the future for a better, pathogen-resistant B. napus.
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Affiliation(s)
- Ting Xiang Neik
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Martin J. Barbetti
- School of Agriculture and Environment and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
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29
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Scheben A, Batley J, Edwards D. Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:149-161. [PMID: 27696619 PMCID: PMC5258866 DOI: 10.1111/pbi.12645] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/24/2016] [Accepted: 09/28/2016] [Indexed: 05/18/2023]
Abstract
In the last decade, the revolution in sequencing technologies has deeply impacted crop genotyping practice. New methods allowing rapid, high-throughput genotyping of entire crop populations have proliferated and opened the door to wider use of molecular tools in plant breeding. These new genotyping-by-sequencing (GBS) methods include over a dozen reduced-representation sequencing (RRS) approaches and at least four whole-genome resequencing (WGR) approaches. The diversity of methods available, each often producing different types of data at different cost, can make selection of the best-suited method seem a daunting task. We review the most common genotyping methods used today and compare their suitability for linkage mapping, genomewide association studies (GWAS), marker-assisted and genomic selection and genome assembly and improvement in crops with various genome sizes and complexity. Furthermore, we give an outline of bioinformatics tools for analysis of genotyping data. WGR is well suited to genotyping biparental cross populations with complex, small- to moderate-sized genomes and provides the lowest cost per marker data point. RRS approaches differ in their suitability for various tasks, but demonstrate similar costs per marker data point. These approaches are generally better suited for de novo applications and more cost-effective when genotyping populations with large genomes or high heterozygosity. We expect that although RRS approaches will remain the most cost-effective for some time, WGR will become more widespread for crop genotyping as sequencing costs continue to decrease.
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Affiliation(s)
- Armin Scheben
- School of Plant Biology and Institute of AgricultureUniversity of Western AustraliaPerthWAAustralia
| | - Jacqueline Batley
- School of Plant Biology and Institute of AgricultureUniversity of Western AustraliaPerthWAAustralia
| | - David Edwards
- School of Plant Biology and Institute of AgricultureUniversity of Western AustraliaPerthWAAustralia
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30
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Guan H, Ali F, Pan Q. Dissection of Recombination Attributes for Multiple Maize Populations Using a Common SNP Assay. FRONTIERS IN PLANT SCIENCE 2017; 8:2063. [PMID: 29250099 PMCID: PMC5714861 DOI: 10.3389/fpls.2017.02063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 11/17/2017] [Indexed: 05/16/2023]
Abstract
Recombination is a vital characteristic for quantitative trait loci mapping and breeding to enhance the yield potential of maize. However, recombination characteristics in globally used segregating populations have never been evaluated at similar genetic marker densities. This study aimed to divulge the characteristics of recombination events, recombinant chromosomal segments, and recombination frequency for four dissimilar populations. These populations were doubled haploid (DH), recombination inbred line (RIL), intermated B73xMo17 (IBM), and multi-parent advanced generation inter-cross (MAGIC), using the Illumina MaizeSNP50 BeadChip to provide markers. Our results revealed that the average number of recombination events was 16, 41, 72, and 86 per line in DH, RIL, IBM, and MAGIC populations, respectively. Accordingly, the average length of recombinant chromosomal segments was 84.8, 47.3, 29.2, and 20.4 Mb in DH, RIL, IBM, and MAGIC populations, respectively. Furtherly, the recombination frequency varied in different genomic regions and population types [DH (0-12.7 cM/Mb), RIL (0-15.5 cM/Mb), IBM (0-24.1 cM/Mb), MAGIC (0-42.3 cM/Mb)]. Utilizing different sub-sets of lines, the recombination bin number and size were analyzed in each population. Additionally, different sub-sets of markers and lines were employed to estimate the recombination bin number and size via formulas for relationship in these populations. The relationship between recombination events and recombination bin length was also examined. Our results contribute to determining the most suitable number of genetic markers, lines in each population, and population type for successful mapping and breeding.
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Affiliation(s)
- Haiying Guan
- Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China
- National Engineering Laboratory of Wheat and Maize, Jinan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Northern Yellow-Huai River Plain, Ministry of Agriculture, Jinan, China
| | - Farhan Ali
- Cereal Crops Research Institute, Nowshera, Pakistan
| | - Qingchun Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Qingchun Pan,
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31
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Mason AS, Snowdon RJ. Oilseed rape: learning about ancient and recent polyploid evolution from a recent crop species. PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18:883-892. [PMID: 27063780 DOI: 10.1111/plb.12462] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 04/06/2016] [Indexed: 05/18/2023]
Abstract
Oilseed rape (Brassica napus) is one of our youngest crop species, arising several times under cultivation in the last few thousand years and completely unknown in the wild. Oilseed rape originated from hybridisation events between progenitor diploid species B. rapa and B. oleracea, both important vegetable species. The diploid progenitors are also ancient polyploids, with remnants of two previous polyploidisation events evident in the triplicated genome structure. This history of polyploid evolution and human agricultural selection makes B. napus an excellent model with which to investigate processes of genomic evolution and selection in polyploid crops. The ease of de novo interspecific hybridisation, responsiveness to tissue culture, and the close relationship of oilseed rape to the model plant Arabidopsis thaliana, coupled with the recent availability of reference genome sequences and suites of molecular cytogenetic and high-throughput genotyping tools, allow detailed dissection of genetic, genomic and phenotypic interactions in this crop. In this review we discuss the past and present uses of B. napus as a model for polyploid speciation and evolution in crop species, along with current and developing analysis tools and resources. We further outline unanswered questions that may now be tractable to investigation.
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Affiliation(s)
- A S Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany.
| | - R J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
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32
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Pandey MK, Roorkiwal M, Singh VK, Ramalingam A, Kudapa H, Thudi M, Chitikineni A, Rathore A, Varshney RK. Emerging Genomic Tools for Legume Breeding: Current Status and Future Prospects. FRONTIERS IN PLANT SCIENCE 2016; 7:455. [PMID: 27199998 PMCID: PMC4852475 DOI: 10.3389/fpls.2016.00455] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 03/24/2016] [Indexed: 05/19/2023]
Abstract
Legumes play a vital role in ensuring global nutritional food security and improving soil quality through nitrogen fixation. Accelerated higher genetic gains is required to meet the demand of ever increasing global population. In recent years, speedy developments have been witnessed in legume genomics due to advancements in next-generation sequencing (NGS) and high-throughput genotyping technologies. Reference genome sequences for many legume crops have been reported in the last 5 years. The availability of the draft genome sequences and re-sequencing of elite genotypes for several important legume crops have made it possible to identify structural variations at large scale. Availability of large-scale genomic resources and low-cost and high-throughput genotyping technologies are enhancing the efficiency and resolution of genetic mapping and marker-trait association studies. Most importantly, deployment of molecular breeding approaches has resulted in development of improved lines in some legume crops such as chickpea and groundnut. In order to support genomics-driven crop improvement at a fast pace, the deployment of breeder-friendly genomics and decision support tools seems appear to be critical in breeding programs in developing countries. This review provides an overview of emerging genomics and informatics tools/approaches that will be the key driving force for accelerating genomics-assisted breeding and ultimately ensuring nutritional and food security in developing countries.
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Affiliation(s)
- Manish K. Pandey
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Vikas K. Singh
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Abirami Ramalingam
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Anu Chitikineni
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
- The University of Western AustraliaCrawley, WA, Australia
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33
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Batley J, Edwards D. The application of genomics and bioinformatics to accelerate crop improvement in a changing climate. CURRENT OPINION IN PLANT BIOLOGY 2016; 30:78-81. [PMID: 26926905 DOI: 10.1016/j.pbi.2016.02.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 02/02/2016] [Accepted: 02/04/2016] [Indexed: 05/22/2023]
Abstract
The changing climate and growing global population will increase pressure on our ability to produce sufficient food. The breeding of novel crops and the adaptation of current crops to the new environment are required to ensure continued food production. Advances in genomics offer the potential to accelerate the genomics based breeding of crop plants. However, relating genomic data to climate related agronomic traits for use in breeding remains a huge challenge, and one which will require coordination of diverse skills and expertise. Bioinformatics, when combined with genomics has the potential to help maintain food security in the face of climate change through the accelerated production of climate ready crops.
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Affiliation(s)
- Jacqueline Batley
- School of Plant Biology and Institute of Agriculture, University of Western Australia, Crawley 6009, Australia
| | - David Edwards
- School of Plant Biology and Institute of Agriculture, University of Western Australia, Crawley 6009, Australia.
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Varshney RK. Exciting journey of 10 years from genomes to fields and markets: Some success stories of genomics-assisted breeding in chickpea, pigeonpea and groundnut. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:98-107. [PMID: 26566828 DOI: 10.1016/j.plantsci.2015.09.009] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/04/2015] [Accepted: 09/07/2015] [Indexed: 05/20/2023]
Abstract
Legume crops such as chickpea, pigeonpea and groundnut, mostly grown in marginal environments, are the major source of nutrition and protein to the human population in Asia and Sub-Saharan Africa. These crops, however, have a low productivity, mainly due to their exposure to several biotic and abiotic stresses in the marginal environments. Until 2005, these crops had limited genomics resources and molecular breeding was very challenging. During the last decade (2005-2015), ICRISAT led demand-driven innovations in genome science and translated the massive genome information in breeding. For instance, large-scale genomic resources including draft genome assemblies, comprehensive genetic and physical maps, thousands of SSR markers, millions of SNPs, several high-throughput as well as low cost marker genotyping platforms have been developed in these crops. After mapping several breeding related traits, several success stories of translational genomics have become available in these legumes. These include development of superior lines with enhanced drought tolerance in chickpea, enhanced and pyramided resistance to Fusarium wilt and Ascochyta blight in chickpea, enhanced resistance to leaf rust in groundnut, improved oil quality in groundnut and utilization of markers for assessing purity of hybrids/parental lines in pigeonpea. Some of these stories together with future prospects have been discussed.
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Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India.
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35
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Gacek K, Bayer PE, Bartkowiak-Broda I, Szala L, Bocianowski J, Edwards D, Batley J. Genome-Wide Association Study of Genetic Control of Seed Fatty Acid Biosynthesis in Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:2062. [PMID: 28163710 PMCID: PMC5247464 DOI: 10.3389/fpls.2016.02062] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/26/2016] [Indexed: 05/03/2023]
Abstract
Fatty acids and their composition in seeds determine oil value for nutritional or industrial purposes and also affect seed germination as well as seedling establishment. To better understand the genetic basis of seed fatty acid biosynthesis in oilseed rape (Brassica napus L.) we applied a genome-wide association study, using 91,205 single nucleotide polymorphisms (SNPs) characterized across a mapping population with high-resolution skim genotyping by sequencing (SkimGBS). We identified a cluster of loci on chromosome A05 associated with oleic and linoleic seed fatty acids. The delineated genomic region contained orthologs of the Arabidopsis thaliana genes known to play a role in regulation of seed fatty acid biosynthesis such as Fatty acyl-ACP thioesterase B (FATB) and Fatty Acid Desaturase (FAD5). This approach allowed us to identify potential functional genes regulating fatty acid composition in this important oil producing crop and demonstrates that this approach can be used as a powerful tool for dissecting complex traits for B. napus improvement programs.
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Affiliation(s)
- Katarzyna Gacek
- Plant Breeding and Acclimatization Institute—National Research Institute, Oilseed Crops Research CentrePoznan, Poland
| | - Philipp E. Bayer
- School of Plant Biology, University of Western AustraliaPerth, WA, Australia
| | - Iwona Bartkowiak-Broda
- Plant Breeding and Acclimatization Institute—National Research Institute, Oilseed Crops Research CentrePoznan, Poland
| | - Laurencja Szala
- Plant Breeding and Acclimatization Institute—National Research Institute, Oilseed Crops Research CentrePoznan, Poland
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznan University of Life SciencesPoznan, Poland
| | - David Edwards
- School of Plant Biology, University of Western AustraliaPerth, WA, Australia
| | - Jacqueline Batley
- School of Plant Biology, University of Western AustraliaPerth, WA, Australia
- *Correspondence: Jacqueline Batley
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36
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Liu J, Wang J, Wang H, Wang W, Zhou R, Mei D, Cheng H, Yang J, Raman H, Hu Q. Multigenic Control of Pod Shattering Resistance in Chinese Rapeseed Germplasm Revealed by Genome-Wide Association and Linkage Analyses. FRONTIERS IN PLANT SCIENCE 2016; 7:1058. [PMID: 27493651 PMCID: PMC4954820 DOI: 10.3389/fpls.2016.01058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 07/06/2016] [Indexed: 05/03/2023]
Abstract
The majority of rapeseed cultivars shatter seeds upon maturity especially under hot-dry and windy conditions, reducing yield and gross margin return to growers. Here, we identified quantitative trait loci (QTL) for resistance to pod shatter in an unstructured diverse panel of 143 rapeseed accessions, and two structured populations derived from bi-parental doubled haploid (DH) and inter-mated (IF2) crosses derived from R1 (resistant to pod shattering) and R2 (prone to pod shattering) accessions. Genome-wide association analysis identified six significant QTL for resistance to pod shatter located on chromosomes A01, A06, A07, A09, C02, and C05. Two of the QTL, qSRI.A09 delimited with the SNP marker Bn-A09-p30171993 (A09) and qSRI.A06 delimited with the SNP marker Bn-A06-p115948 (A06) could be repeatedly detected across environments in a diversity panel, DH and IF2 populations, suggesting that at least two loci on chromosomes A06 and A09 were the main contributors to pod shatter resistance in Chinese germplasm. Significant SNP markers identified in this study especially those that appeared repeatedly across environments provide a cost-effective and an efficient method for introgression and pyramiding of favorable alleles for pod shatter resistance via marker-assisted selection in rapeseed improvement programs.
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Affiliation(s)
- Jia Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Jun Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
- Graduate School of Chinese Academy of Agricultural SciencesBeijing, China
| | - Hui Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Wenxiang Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Rijin Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Desheng Mei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Hongtao Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Juan Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
| | - Harsh Raman
- Graham Centre for Agricultural Innovation (an Alliance between NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga Agricultural InstituteWagga Wagga, NSW, Australia
- *Correspondence: Harsh Raman
| | - Qiong Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhan, China
- Qiong Hu
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37
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Kale SM, Jaganathan D, Ruperao P, Chen C, Punna R, Kudapa H, Thudi M, Roorkiwal M, Katta MA, Doddamani D, Garg V, Kishor PBK, Gaur PM, Nguyen HT, Batley J, Edwards D, Sutton T, Varshney RK. Prioritization of candidate genes in "QTL-hotspot" region for drought tolerance in chickpea (Cicer arietinum L.). Sci Rep 2015; 5:15296. [PMID: 26478518 PMCID: PMC4609953 DOI: 10.1038/srep15296] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/22/2015] [Indexed: 01/20/2023] Open
Abstract
A combination of two approaches, namely QTL analysis and gene enrichment analysis were used to identify candidate genes in the “QTL-hotspot” region for drought tolerance present on the Ca4 pseudomolecule in chickpea. In the first approach, a high-density bin map was developed using 53,223 single nucleotide polymorphisms (SNPs) identified in the recombinant inbred line (RIL) population of ICC 4958 (drought tolerant) and ICC 1882 (drought sensitive) cross. QTL analysis using recombination bins as markers along with the phenotyping data for 17 drought tolerance related traits obtained over 1–5 seasons and 1–5 locations split the “QTL-hotspot” region into two subregions namely “QTL-hotspot_a” (15 genes) and “QTL-hotspot_b” (11 genes). In the second approach, gene enrichment analysis using significant marker trait associations based on SNPs from the Ca4 pseudomolecule with the above mentioned phenotyping data, and the candidate genes from the refined “QTL-hotspot” region showed enrichment for 23 genes. Twelve genes were found common in both approaches. Functional validation using quantitative real-time PCR (qRT-PCR) indicated four promising candidate genes having functional implications on the effect of “QTL-hotspot” for drought tolerance in chickpea.
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Affiliation(s)
- Sandip M Kale
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India
| | - Deepa Jaganathan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India.,Osmania University, Department of Genetics, Hyderabad, 500007, India
| | - Pradeep Ruperao
- The University of Western Australia, School of Plant Biology and the Institute of Agriculture, Crawley, 6009, Australia.,University of Queensland, School of Agriculture and Food Science, Queensland, 4072, Australia
| | - Charles Chen
- Oklahoma State University, Department of Biochemistry and Molecular Biology, Stillwater, 74074, USA
| | - Ramu Punna
- Cornell University, Biotechnology Building, Ithaca, 14853, USA
| | - Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India
| | - Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India
| | - Mohan Avsk Katta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India
| | - Dadakhalandar Doddamani
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India
| | - Vanika Garg
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India
| | - P B Kavi Kishor
- Osmania University, Department of Genetics, Hyderabad, 500007, India
| | - Pooran M Gaur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India
| | - Henry T Nguyen
- University of Missouri, National Center for Soybean Biotechnology and Division of Plant Sciences, Columbia, 65211, USA
| | - Jacqueline Batley
- The University of Western Australia, School of Plant Biology and the Institute of Agriculture, Crawley, 6009, Australia
| | - David Edwards
- The University of Western Australia, School of Plant Biology and the Institute of Agriculture, Crawley, 6009, Australia
| | - Tim Sutton
- South Australian Research and Development Institute, Adelaide, 5001, Australia.,University of Adelaide, Australia and School of Agriculture, Adelaide, 5064, Australia
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India.,The University of Western Australia, School of Plant Biology and the Institute of Agriculture, Crawley, 6009, Australia
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