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Paulino JFDC, de Almeida CP, Bueno CJ, Song Q, Fritsche-Neto R, Carbonell SAM, Chiorato AF, Benchimol-Reis LL. Genome-Wide Association Study Reveals Genomic Regions Associated with Fusarium Wilt Resistance in Common Bean. Genes (Basel) 2021; 12:765. [PMID: 34069884 PMCID: PMC8157364 DOI: 10.3390/genes12050765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/13/2021] [Accepted: 05/13/2021] [Indexed: 12/31/2022] Open
Abstract
Fusarium wilt (Fusarium oxysporum f. sp. phaseoli, Fop) is one of the main fungal soil diseases in common bean. The aim of the present study was to identify genomic regions associated with Fop resistance through genome-wide association studies (GWAS) in a Mesoamerican Diversity Panel (MDP) and to identify potential common bean sources of Fop's resistance. The MDP was genotyped with BARCBean6K_3BeadChip and evaluated for Fop resistance with two different monosporic strains using the root-dip method. Disease severity rating (DSR) and the area under the disease progress curve (AUDPC), at 21 days after inoculation (DAI), were used for GWAS performed with FarmCPU model. The p-value of each SNP was determined by resampling method and Bonferroni test. For UFV01 strain, two significant single nucleotide polymorphisms (SNPs) were mapped on the Pv05 and Pv11 for AUDPC, and the same SNP (ss715648096) on Pv11 was associated with AUDPC and DSR. Another SNP, mapped on Pv03, showed significance for DSR. Regarding IAC18001 strain, significant SNPs on Pv03, Pv04, Pv05, Pv07 and on Pv01, Pv05, and Pv10 were observed. Putative candidate genes related to nucleotide-binding sites and carboxy-terminal leucine-rich repeats were identified. The markers may be important future tools for genomic selection to Fop disease resistance in beans.
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Affiliation(s)
| | - Caléo Panhoca de Almeida
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico, Campinas 13075-630, SP, Brazil; (J.F.d.C.P.); (C.P.d.A.)
| | - César Júnior Bueno
- Centro Avançado de Pesquisa em Proteção de Plantas e Saúde Animal, Instituto Biológico, Campinas 13101-680, SP, Brazil;
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, US Department of Agriculture, Agricultural Research Service (USDA-ARS), Beltsville, MD 20705, USA;
| | - Roberto Fritsche-Neto
- Department of Genetics, ‘Luiz de Queiroz’ Agriculture College, University of Sao Paulo, Piracicaba 13418-900, SP, Brazil;
| | | | - Alisson Fernando Chiorato
- Centro de Grãos e Fibras, Instituto Agronômico, Campinas 13075-630, SP, Brazil; (S.A.M.C.); (A.F.C.)
| | - Luciana Lasry Benchimol-Reis
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico, Campinas 13075-630, SP, Brazil; (J.F.d.C.P.); (C.P.d.A.)
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202
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Sulli M, Barchi L, Toppino L, Diretto G, Sala T, Lanteri S, Rotino GL, Giuliano G. An Eggplant Recombinant Inbred Population Allows the Discovery of Metabolic QTLs Controlling Fruit Nutritional Quality. FRONTIERS IN PLANT SCIENCE 2021; 12:638195. [PMID: 34079565 PMCID: PMC8166230 DOI: 10.3389/fpls.2021.638195] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/22/2021] [Indexed: 06/02/2023]
Abstract
Eggplant (Solanum melongena L.) represents the third most important crop of the Solanaceae family and is an important component of our daily diet. A population of 164 F6 recombinant inbred lines (RILs), derived from two eggplant lines differing with respect to several key agronomic traits, "305E40" and "67/3," was grown to the commercial maturation stage, and fruits were harvested, separated into peel and flesh, and subjected to liquid chromatography Liquid Chromatography/Mass Spectrometry (LC/MS) analysis. Through a combination of untargeted and targeted metabolomics approaches, a number of metabolites belonging to the glycoalkaloid, anthocyanin, and polyamine classes and showing a differential accumulation in the two parental lines and F1 hybrid were identified. Through metabolic profiling of the RILs, we identified several metabolomic quantitative trait loci (mQTLs) associated with the accumulation of those metabolites. Each of the metabolic traits proved to be controlled by one or more quantitative trait loci (QTLs); for most of the traits, one major mQTL (phenotypic variation explained [PVE] ≥ 10%) was identified. Data on mQTL mapping and dominance-recessivity relationships of measured compounds in the parental lines and F1 hybrid, as well as an analysis of the candidate genes underlying the QTLs and of their sequence differences in the two parental lines, suggested a series of candidate genes underlying the traits under study.
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Affiliation(s)
- Maria Sulli
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Lorenzo Barchi
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics and Breeding, University of Turin, Grugliasco, Italy
| | - Laura Toppino
- CREA, Council for Agricultural and Economics Research, Research Centre for Genomics and Bioinformatics, Montanaso Lombardo, Italy
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Tea Sala
- CREA, Council for Agricultural and Economics Research, Research Centre for Genomics and Bioinformatics, Montanaso Lombardo, Italy
| | - Sergio Lanteri
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics and Breeding, University of Turin, Grugliasco, Italy
| | - Giuseppe Leonardo Rotino
- CREA, Council for Agricultural and Economics Research, Research Centre for Genomics and Bioinformatics, Montanaso Lombardo, Italy
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
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203
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Sun X, Gao Y, Lu Y, Zhang X, Luo S, Li X, Liu M, Feng D, Gu A, Chen X, Xuan S, Wang Y, Shen S, Bonnema G, Zhao J. Genetic analysis of the "head top shape" quality trait of Chinese cabbage and its association with rosette leaf variation. HORTICULTURE RESEARCH 2021; 8:106. [PMID: 33931629 PMCID: PMC8087666 DOI: 10.1038/s41438-021-00541-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 02/10/2021] [Accepted: 03/05/2021] [Indexed: 05/08/2023]
Abstract
The agricultural and consumer quality of Chinese cabbage is determined by its shape. The shape is defined by the folding of the heading leaves, which defines the head top shape (HTS). The overlapping HTS, in which the heading leaves curve inward and overlap at the top, is the shape preferred by consumers. To understand the genetic regulation of HTS, we generated a large segregating F2 population from a cross between pak choi and Chinese cabbage, with phenotypes ranging from nonheading to heading with either outward curving or inward curving overlapping heading leaves. HTS was correlated with plant height, outer/rosette leaf length, and petiole length. A high-density genetic map was constructed. Quantitative trait locus (QTL) analysis resulted in the identification of 22 QTLs for leafy head-related traits, which included five HTS QTLs. Bulked segregant analysis (BSA) was used to confirm HTS QTLs and identify candidate genes based on informative single-nucleotide polymorphisms. Interestingly, the HTS QTLs colocalized with QTLs for plant height, outer/rosette leaf, and petiole length, consistent with the observed phenotypic correlations. Combined QTL analysis and BSA laid a foundation for molecular marker-assisted breeding of Chinese cabbage HTS and directions for further research on the genetic regulation of this trait.
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Affiliation(s)
- Xiaoxue Sun
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Ying Gao
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Yin Lu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Xiaomeng Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Shuangxia Luo
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Xing Li
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Mengyang Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Daling Feng
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Aixia Gu
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Xueping Chen
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Shuxin Xuan
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Yanhua Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China
| | - Shuxing Shen
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China.
| | - Guusje Bonnema
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China.
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands.
| | - Jianjun Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, 071000, Baoding, China.
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204
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Sandoya GV, Truco MJ, Bertier LD, Subbarao KV, Simko I, Hayes RJ, Michelmore RW. Genetics of Partial Resistance Against Verticillium dahliae Race 2 in Wild and Cultivated Lettuce. PHYTOPATHOLOGY 2021; 111:842-849. [PMID: 33141646 DOI: 10.1094/phyto-09-20-0396-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Lettuce (Lactuca sativa) is one of the most economically important vegetables in the United States, with approximately 50% of the domestic production concentrated in the Salinas Valley of California. Verticillium wilt, caused by races 1 and 2 of the fungal pathogen Verticillium dahliae, poses a major threat to lettuce production in this area. Although resistance governed by a single dominant gene against race 1 has previously been identified and is currently being incorporated into commercial cultivars, identification of resistance against race 2 has been challenging and no lines with complete resistance have been identified. In this study, we screened germplasm for resistance and investigated the genetics of partial resistance against race 2 using three mapping populations derived from crosses involving L. sativa × L. sativa and L. serriola × L. sativa. The inheritance of resistance in Lactuca species against race 2 is complex but a common quantitative trait locus (QTL) on linkage group 6, designated qVERT6.1 (quantitative Verticillium dahliae resistance on LG 6, first QTL), was detected in multiple populations. Additional race 2 resistance QTLs located in several linkage groups were detected in individual populations and environments. Because resistance in lettuce against race 2 is polygenic with a large genotype by environment interaction, breeding programs to incorporate these resistance genes should be aware of this complexity as they implement strategies to control race 2.
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Affiliation(s)
- Germán V Sandoya
- Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616
| | - Maria José Truco
- Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616
| | - Lien D Bertier
- Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616
| | - Krishna V Subbarao
- Plant Pathology Department, University of California, Davis, Salinas, CA 93905
| | - Ivan Simko
- Crop Improvement and Protection Research Unit, U.S. Department of Agriculture Agricultural Research Service, Salinas, CA 93905
| | - Ryan J Hayes
- Crop Improvement and Protection Research Unit, U.S. Department of Agriculture Agricultural Research Service, Salinas, CA 93905
| | - Richard W Michelmore
- Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616
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205
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The recombination landscape and multiple QTL mapping in a Solanum tuberosum cv. 'Atlantic'-derived F 1 population. Heredity (Edinb) 2021; 126:817-830. [PMID: 33753876 PMCID: PMC8102480 DOI: 10.1038/s41437-021-00416-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 02/01/2023] Open
Abstract
There are many challenges involved with the genetic analyses of autopolyploid species, such as the tetraploid potato, Solanum tuberosum (2n = 4x = 48). The development of new analytical methods has made it valuable to re-analyze an F1 population (n = 156) derived from a cross involving 'Atlantic', a widely grown chipping variety in the USA. A fully integrated genetic map with 4285 single nucleotide polymorphisms, spanning 1630 cM, was constructed with MAPpoly software. We observed that bivalent configurations were the most abundant ones (51.0~72.4% depending on parent and linkage group), though multivalent configurations were also observed (2.2~39.2%). Seven traits were evaluated over four years (2006-8 and 2014) and quantitative trait loci (QTL) mapping was carried out using QTLpoly software. Based on a multiple-QTL model approach, we detected 21 QTL for 15 out of 27 trait-year combination phenotypes. A hotspot on linkage group 5 was identified with co-located QTL for maturity, plant yield, specific gravity, and internal heat necrosis resistance evaluated over different years. Additional QTL for specific gravity and dry matter were detected with maturity-corrected phenotypes. Among the genes around QTL peaks, we found those on chromosome 5 that have been previously implicated in maturity (StCDF1) and tuber formation (POTH1). These analyses have the potential to provide insights into the biology and breeding of tetraploid potato and other autopolyploid species.
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206
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Haghdoust R, Singh D, Park RF, Dracatos PM. Characterizing the Genetic Architecture of Nonhost Resistance in Barley Using Pathogenically Diverse Puccinia Isolates. PHYTOPATHOLOGY 2021; 111:684-694. [PMID: 32931394 DOI: 10.1094/phyto-05-20-0193-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Barley is an intermediate or near nonhost to many cereal rust pathogens that infect grasses, making it a highly suitable model to understand the evolution and genetic basis of nonhost resistance (NHR) in plants. To characterize the genetic architecture of NHR in barley, we used the Oregon Wolfe Barley doubled haploid and Morex × SusPtrit recombinant inbred line mapping populations. To elicit a wide array of NHR responses, we tested 492 barley accessions and both mapping populations with pathogenically diverse cereal rust isolates representing distinct formae speciales adapted to Avena, Hordeum, Triticum, and Lolium spp.: P. coronata f. sp. avenae (oat crown rust pathogen) and P. coronata f. sp. lolii (ryegrass crown rust pathogen), P. graminis f. sp. avenae (oat stem rust pathogen) and P. graminis f. sp. lolii (the ryegrass stem rust pathogen), and P. striiformis f. sp. tritici (wheat stripe rust pathogen) and P. striiformis f. sp. pseudo-hordei (barley grass stripe rust pathogen). With the exception of P. coronata f. sp. lolii and P. coronata f. sp. avenae, susceptibility and segregation for NHR was observed in the barley accessions and both mapping populations. Quantitative trait loci (QTLs) for NHR were mapped on all seven chromosomes. NHR in barley to the heterologous rusts tested was attributable to a combination of QTLs with either or both overlapping and distinct specificities. Across both mapping populations, broadly effective NHR loci were also identified that likely play a role in host specialization.
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Affiliation(s)
- R Haghdoust
- Plant Breeding Institute, University of Sydney, Cobbitty, Narellan, New South Wales 2567, Australia
| | - D Singh
- Plant Breeding Institute, University of Sydney, Cobbitty, Narellan, New South Wales 2567, Australia
| | - R F Park
- Plant Breeding Institute, University of Sydney, Cobbitty, Narellan, New South Wales 2567, Australia
| | - P M Dracatos
- Plant Breeding Institute, University of Sydney, Cobbitty, Narellan, New South Wales 2567, Australia
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207
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Mao M, Popli T, Jeanne M, Hoff K, Sen S, Gould DB. Identification of fibronectin 1 as a candidate genetic modifier in a Col4a1 mutant mouse model of Gould syndrome. Dis Model Mech 2021; 14:dmm048231. [PMID: 34424299 PMCID: PMC8106953 DOI: 10.1242/dmm.048231] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/02/2021] [Indexed: 12/12/2022] Open
Abstract
Collagen type IV alpha 1 and alpha 2 (COL4A1 and COL4A2) are major components of almost all basement membranes. COL4A1 and COL4A2 mutations cause a multisystem disorder that can affect any organ but typically involves the cerebral vasculature, eyes, kidneys and skeletal muscles. In recent years, patient advocacy and family support groups have united under the name of Gould syndrome. The manifestations of Gould syndrome are highly variable, and animal studies suggest that allelic heterogeneity and genetic context contribute to the clinical variability. We previously characterized a mouse model of Gould syndrome caused by a Col4a1 mutation in which the severities of ocular anterior segment dysgenesis (ASD), myopathy and intracerebral hemorrhage (ICH) were dependent on genetic background. Here, we performed a genetic modifier screen to provide insight into the mechanisms contributing to Gould syndrome pathogenesis and identified a single locus [modifier of Gould syndrome 1 (MoGS1)] on Chromosome 1 that suppressed ASD. A separate screen showed that the same locus ameliorated myopathy. Interestingly, MoGS1 had no effect on ICH, suggesting that this phenotype could be mechanistically distinct. We refined the MoGS1 locus to a 4.3 Mb interval containing 18 protein-coding genes, including Fn1, which encodes the extracellular matrix component fibronectin 1. Molecular analysis showed that the MoGS1 locus increased Fn1 expression, raising the possibility that suppression is achieved through a compensatory extracellular mechanism. Furthermore, we found evidence of increased integrin-linked kinase levels and focal adhesion kinase phosphorylation in Col4a1 mutant mice that is partially restored by the MoGS1 locus, implicating the involvement of integrin signaling. Taken together, our results suggest that tissue-specific mechanistic heterogeneity contributes to the variable expressivity of Gould syndrome and that perturbations in integrin signaling may play a role in ocular and muscular manifestations.
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Affiliation(s)
- Mao Mao
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Tanav Popli
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Marion Jeanne
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Kendall Hoff
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Saunak Sen
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Preventive Medicine, University of Tennessee Health Science Center, 66 North Pauline St, Memphis, TN 38163, USA
| | - Douglas B. Gould
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA 94143, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
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208
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Mori M, Maki K, Kawahata T, Kawahara D, Kato Y, Yoshida T, Nagasawa H, Sato H, Nagano AJ, Bethke PC, Kato K. Mapping of QTLs controlling epicotyl length in adzuki bean ( Vigna angularis). BREEDING SCIENCE 2021; 71:208-216. [PMID: 34377069 PMCID: PMC8329883 DOI: 10.1270/jsbbs.20093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 12/02/2020] [Indexed: 05/14/2023]
Abstract
Epicotyl length (ECL) of adzuki bean (Vigna angularis) affects the efficiency of mechanized weeding and harvest. The present study investigated the genetic factors controlling ECL. An F2 population derived from a cross between the breeding line 'Tokei1121' (T1121, long epicotyls) and the cultivar 'Erimo167' (common epicotyls) was phenotyped for ECL and genotyped using simple sequence repeats (SSRs) and single-nucleotide polymorphism (SNP) markers. A molecular linkage map was generated and fifty-two segregating markers, including 27 SSRs and 25 SNPs, were located on seven linkage groups (LGs) at a LOD threshold value of 3.0. Four quantitative trait loci (QTLs) for ECL, with LOD scores of 4.0, 3.4, 4.8 and 6.4, were identified on LGs 2, 4, 7 and 10, respectively; together, these four QTLs accounted for 49.3% of the phenotypic variance. The segregation patterns observed in F5 residual heterozygous lines at qECL10 revealed that a single recessive gene derived from T1121 contributed to the longer ECL phenotype. Using five insertion and deletion markers, this gene was fine mapped to a ~255 kb region near the end of LG10. These findings will facilitate marker-assisted selection for breeding in the adzuki bean and contribute to an understanding of the mechanisms associated with epicotyl elongation.
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Affiliation(s)
- Masahiko Mori
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555, Japan
- Corresponding authors (e-mail: and )
| | - Kento Maki
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555, Japan
| | - Tsubasa Kawahata
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555, Japan
| | - Daigo Kawahara
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555, Japan
| | - Yuta Kato
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555, Japan
| | - Toru Yoshida
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555, Japan
| | - Hidetaka Nagasawa
- Tokachi Agricultural Experiment Station, Agricultural Research Department, Hokkaido Research Organization, Memuro, Hokkaido 082-0081, Japan
| | - Hitoshi Sato
- Tokachi Agricultural Experiment Station, Agricultural Research Department, Hokkaido Research Organization, Memuro, Hokkaido 082-0081, Japan
- Plant Genetic Resources Division, Central Agricultural Experiment Station, Agricultural Research Department, Hokkaido Research Organization, Takikawa, Hokkaido 073-0013, Japan
| | - Atsushi J. Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga 520-2194, Japan
| | - Paul C. Bethke
- Vegetable Crops Research Unit, USDA Agricultural Research Service, Madison, Wisconsin 53706, USA
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Kiyoaki Kato
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Nishi 2-11 Inada, Obihiro, Hokkaido 080-8555, Japan
- Corresponding authors (e-mail: and )
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209
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Chen J, Leach L, Yang J, Zhang F, Tao Q, Dang Z, Chen Y, Luo Z. A tetrasomic inheritance model and likelihood-based method for mapping quantitative trait loci in autotetraploid species. THE NEW PHYTOLOGIST 2021; 230:387-398. [PMID: 31913501 PMCID: PMC7984458 DOI: 10.1111/nph.16413] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 12/20/2019] [Indexed: 06/10/2023]
Abstract
Dissecting the genetic architecture of quantitative traits in autotetraploid species is a methodologically challenging task, but a pivotally important goal for breeding globally important food crops, including potato and blueberry, and ornamental species such as rose. Mapping quantitative trait loci (QTLs) is now a routine practice in diploid species but is far less advanced in autotetraploids, largely due to a lack of analytical methods that account for the complexities of tetrasomic inheritance. We present a novel likelihood-based method for QTL mapping in outbred segregating populations of autotetraploid species. The method accounts properly for sophisticated features of gene segregation and recombination in an autotetraploid meiosis. It may model and analyse molecular marker data with or without allele dosage information, such as that from microarray or sequencing experiments. The method developed outperforms existing bivalent-based methods, which may fail to model and analyse the full spectrum of experimental data, in the statistical power of QTL detection, and accuracy of QTL location, as demonstrated by an intensive simulation study and analysis of data sets collected from a segregating population of potato (Solanum tuberosum). The study enables QTL mapping analysis to be conducted in autotetraploid species under a rigorous tetrasomic inheritance model.
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Affiliation(s)
- Jing Chen
- School of BiosciencesThe University of BirminghamBirminghamB15 2TTUK
| | - Lindsey Leach
- School of BiosciencesThe University of BirminghamBirminghamB15 2TTUK
| | - Jixuan Yang
- Institute of BiostatisticsFudan UniversityShanghai200433China
| | - Fengjun Zhang
- Institute of BiostatisticsFudan UniversityShanghai200433China
- Qinghai Academy of Agricultural and Forestry SciencesXiningQinghai810016China
| | - Qin Tao
- Institute of BiostatisticsFudan UniversityShanghai200433China
| | - Zhenyu Dang
- Institute of BiostatisticsFudan UniversityShanghai200433China
| | - Yue Chen
- Institute of BiostatisticsFudan UniversityShanghai200433China
| | - Zewei Luo
- School of BiosciencesThe University of BirminghamBirminghamB15 2TTUK
- Institute of BiostatisticsFudan UniversityShanghai200433China
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Yoneya Y, Wakabayashi T, Kato K. The temperature sensitive hybrid breakdown 1 induces low temperature-dependent intrasubspecific hybrid breakdown in rice. BREEDING SCIENCE 2021; 71:268-276. [PMID: 34377075 PMCID: PMC8329891 DOI: 10.1270/jsbbs.20129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/07/2021] [Indexed: 06/13/2023]
Abstract
Hybrid breakdown (HB) is an important type of post-zygotic reproductive barrier that inhibits hybrid production during the process of cross-breeding. A novel low temperature-dependent HB was identified in a chromosomal segment substitution line (CSSL) library derived from a cross of two rice (Oryza sativa L. japonica) cultivars, Yukihikari and Kirara397. A set of weakness symptoms in a target CSSL was observed at 23°C, but was rescued at 27°C and/or 30°C. Genetic analysis of HB using an F2:3 population of a cross between a target CSSL and Kirara397 found that a recessive temperature sensitive hybrid breakdown1 (thb1) gene from Yukihikari caused HB in the genetic background of Kirara397. Molecular mapping showed that thb1 was located within a 199-kb fragment on chromosome 6. A genetic study of F2 populations of reciprocal crosses between Yukihikari and Kirara397 confirmed that this HB was induced by the interaction of two recessive genes. These results provide important clues to further dissect the mechanism of generation of a novel temperature sensitive HB in rice intrasubspecific crosses and suggest that these linked markers will useful in rice breeding.
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Affiliation(s)
- Yuuki Yoneya
- Department of Agro-Environmental Science, Obihiro University of Agriculture
and Veterinary Medicine, Nishi 2-11 Inada, Obihiro, Hokkaido
080-8555, Japan
| | - Tae Wakabayashi
- Department of Agro-Environmental Science, Obihiro University of Agriculture
and Veterinary Medicine, Nishi 2-11 Inada, Obihiro, Hokkaido
080-8555, Japan
| | - Kiyoaki Kato
- Department of Agro-Environmental Science, Obihiro University of Agriculture
and Veterinary Medicine, Nishi 2-11 Inada, Obihiro, Hokkaido
080-8555, Japan
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211
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Zhang S, Du H, Ma Y, Li H, Kan G, Yu D. Linkage and association study discovered loci and candidate genes for glycinin and β-conglycinin in soybean (Glycine max L. Merr.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1201-1215. [PMID: 33464377 DOI: 10.1007/s00122-021-03766-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
KEY MESSAGE Linkage mapping and GWAS identified 67 QTLs related to soybean glycinin, β-conglycinin and relevant traits. Polymorphisms of the candidate gene Gy1 promoter were associated with the glycinin content in soybean. The major components of storage proteins in soybean seeds are glycinin and β-conglycinin, which play important roles in determining protein nutrition and soy food processing properties. Increasing the protein content while improving the ratio of glycinin to β-conglycinin is substantially important for soybean protein improvement. To investigate the genetic mechanism of storage protein subunits, 184 recombinant inbred lines (RILs) derived from a cross of Kefeng No. 1 and Nannong 1138-2 and 211 diverse soybean cultivars were used to detect loci related to glycinin (11S), β-conglycinin (7S), the sum of glycinin and β-conglycinin (SGC), and the ratio of glycinin to β-conglycinin (RGC). Sixty-seven QTLs and 11 hot genomic regions were identified as affecting the four traits. One genetic region (q10-1) on chromosome 10 was associated with multiple traits by both linkage and association analysis. Eight genes in 11 hot genomic regions might be related to soybean protein subunit. The candidate gene analysis showed that polymorphisms in Gy1 promoters were significantly correlated with the 11S content. The QTLs and candidate genes identified in the present study allow for further understanding the genetic basis of 11S and 7S regulation and provide useful information for marker-assisted selection (MAS) in soybean quality improvement.
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Affiliation(s)
- Shanshan Zhang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hongyang Du
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yujie Ma
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haiyang Li
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Guizhen Kan
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China.
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China.
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212
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Desiderio F, Bourras S, Mazzucotelli E, Rubiales D, Keller B, Cattivelli L, Valè G. Characterization of the Resistance to Powdery Mildew and Leaf Rust Carried by the Bread Wheat Cultivar Victo. Int J Mol Sci 2021; 22:ijms22063109. [PMID: 33803699 PMCID: PMC8003046 DOI: 10.3390/ijms22063109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/02/2021] [Accepted: 03/12/2021] [Indexed: 11/28/2022] Open
Abstract
Leaf rust and powdery mildew are two important foliar diseases in wheat. A recombinant inbred line (RIL) population, obtained by crossing two bread wheat cultivars (‘Victo’ and ‘Spada’), was evaluated for resistance to the two pathogens at seedling stage. Upon developing a genetic map of 8726 SNP loci, linkage analysis identified three resistance Quantitative Trait Loci (QTLs), with ‘Victo’ contributing the resistant alleles to all loci. One major QTL (QPm.gb-7A) was detected in response to Blumeria graminis on chromosome 7A, which explained 90% of phenotypic variation (PV). The co-positional relationship with known powdery mildew (Pm) resistance loci suggested that a new source of resistance was identified in T. aestivum. Two QTLs were detected in response to Puccinia triticina: a major gene on chromosome 5D (QLr.gb-5D), explaining a total PV of about 59%, and a minor QTL on chromosome 2B (QLr.gb-2B). A positional relationship was observed between the QLr.gb-5D with the known Lr1 gene, but polymorphisms were found between the cloned Lr1 and the corresponding ‘Victo’ allele, suggesting that QLr.gb-5D could represent a new functional Lr1 allele. Lastly, upon anchoring the QTL on the T. aestivum reference genome, candidate genes were hypothesized on the basis of gene annotation and in silico gene expression analysis.
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Affiliation(s)
- Francesca Desiderio
- CREA Research Centre for Genomics and Bioinformatics, 29017 Fiorenzuola d’Arda, Italy; (E.M.); (L.C.)
- Correspondence: ; Tel.: +39-0523-983758
| | - Salim Bourras
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland; (S.B.); (B.K.)
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75651 Uppsala, Sweden
| | - Elisabetta Mazzucotelli
- CREA Research Centre for Genomics and Bioinformatics, 29017 Fiorenzuola d’Arda, Italy; (E.M.); (L.C.)
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, 14004 Córdoba, Spain;
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland; (S.B.); (B.K.)
| | - Luigi Cattivelli
- CREA Research Centre for Genomics and Bioinformatics, 29017 Fiorenzuola d’Arda, Italy; (E.M.); (L.C.)
| | - Giampiero Valè
- DiSIT—Dipartimento di Scienze e Innovazione Tecnologica, Università del Piemonte Orientale, 13100 Vercelli, Italy;
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213
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Mapping of Quantitative Trait Loci (QTL) Associated with Plant Freezing Tolerance and Cold Acclimation. Methods Mol Biol 2021. [PMID: 32607976 DOI: 10.1007/978-1-0716-0660-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Most agronomic traits are determined by quantitative trait loci (QTL) and exhibit continuous distribution in natural or especially built segregating populations. The genetic architecture and the hereditary characteristics of these traits are much more complicated than those of oligogenic traits and need adapted strategies for deciphering. The model plant Arabidopsis thaliana is widely studied for quantitative traits, especially via the utilization of genetic natural diversity. Here we describe a QTL-mapping protocol for analyzing freezing tolerance after cold acclimation in this species, based on its specific genetic tools. Nevertheless, this approach can be applied for the elucidation of complex traits in others species.
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214
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Yang M, Wang C, Hassan MA, Li F, Xia X, Shi S, Xiao Y, He Z. QTL mapping of root traits in wheat under different phosphorus levels using hydroponic culture. BMC Genomics 2021; 22:174. [PMID: 33706703 PMCID: PMC7953759 DOI: 10.1186/s12864-021-07425-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 02/04/2021] [Indexed: 12/03/2022] Open
Abstract
Background Phosphorus (P) is an important in ensuring plant morphogenesis and grain quality, therefore an efficient root system is crucial for P-uptake. Identification of useful loci for root morphological and P uptake related traits at seedling stage is important for wheat breeding. The aims of this study were to evaluate phenotypic diversity of Yangmai 16/Zhongmai 895 derived doubled haploid (DH) population for root system architecture (RSA) and biomass related traits (BRT) in different P treatments at seedling stage using hydroponic culture, and to identify QTL using 660 K SNP array based high-density genetic map. Results All traits showed significant variations among the DH lines with high heritabilities (0.76 to 0.91) and high correlations (r = 0.59 to 0.98) among all traits. Inclusive composite interval mapping (ICIM) identified 34 QTL with 4.64–20.41% of the phenotypic variances individually, and the log of odds (LOD) values ranging from 2.59 to 10.43. Seven QTL clusters (C1 to C7) were mapped on chromosomes 3DL, 4BS, 4DS, 6BL, 7AS, 7AL and 7BL, cluster C5 on chromosome 7AS (AX-109955164 - AX-109445593) with pleiotropic effect played key role in modulating root length (RL), root tips number (RTN) and root surface area (ROSA) under low P condition, with the favorable allele from Zhongmai 895. Conclusions This study carried out an imaging pipeline-based rapid phenotyping of RSA and BRT traits in hydroponic culture. It is an efficient approach for screening of large populations under different nutrient conditions. Four QTL on chromosomes 6BL (2) and 7AL (2) identified in low P treatment showed positive additive effects contributed by Zhongmai 895, indicating that Zhongmai 895 could be used as parent for P-deficient breeding. The most stable QTL QRRS.caas-4DS for ratio of root to shoot dry weight (RRS) harbored the stable genetic region with high phenotypic effect, and QTL clusters on 7A might be used for speedy selection of genotypes for P-uptake. SNPs closely linked to QTLs and clusters could be used to improve nutrient-use efficiency. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07425-4.
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Affiliation(s)
- Mengjiao Yang
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Cairong Wang
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.,Agricultural Research Institute of Yili, Yili, 835000, Xinjiang, China
| | - Muhammad Adeel Hassan
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Faji Li
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Shubing Shi
- College of Agriculture, Xinjiang Agricultural University, Urumqi, 830052, Xinjiang, China
| | - Yonggui Xiao
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.,International Maize and Wheat Improvement Centre (CIMMYT) China Office, c/o CAAS, Beijing, 100081, China
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215
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Wilson IW, Moncuquet P, Ellis M, White RG, Zhu QH, Stiller W, Llewellyn D. Characterization and Genetic Mapping of Black Root Rot Resistance in Gossypium arboreum L. Int J Mol Sci 2021; 22:ijms22052642. [PMID: 33807984 PMCID: PMC7961528 DOI: 10.3390/ijms22052642] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 11/16/2022] Open
Abstract
Black root rot (BRR) is an economically important disease of cotton and other crops, especially in cooler regions with short growing seasons. Symptoms include black discoloration of the roots, reduced number of lateral roots and stunted or slow plant growth. The cultivated tetraploid Gossypium species are susceptible to BRR. Resistance to BRR was identified in G. arboreum accession BM13H and is associated with reduced and restricted hyphal growth and less sporulation. Transcriptome analysis indicates that BM13H responds to infection at early time points 2- and 3-days post-inoculation, but by day 5, few differentially expressed genes are observed between infected and uninfected roots. Inheritance of BM13H resistance to BRR was evaluated in an F6 recombinant inbred population and shows a single semi-dominant locus conferring resistance that was fine mapped to a region on chromosome 1, containing ten genes including five putative resistance-like genes.
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Affiliation(s)
- Iain W. Wilson
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2061, Australia; (P.M.); (R.G.W.); (Q.-H.Z.); (D.L.)
- Correspondence:
| | - Philippe Moncuquet
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2061, Australia; (P.M.); (R.G.W.); (Q.-H.Z.); (D.L.)
| | - Marc Ellis
- 133 Route de Beauregard, 74540 Gruffy, France;
| | - Rosemary G. White
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2061, Australia; (P.M.); (R.G.W.); (Q.-H.Z.); (D.L.)
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2061, Australia; (P.M.); (R.G.W.); (Q.-H.Z.); (D.L.)
| | - Warwick Stiller
- CSIRO Agriculture and Food, Locked Bag 59, Narrabri, NSW 2390, Australia;
| | - Danny Llewellyn
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2061, Australia; (P.M.); (R.G.W.); (Q.-H.Z.); (D.L.)
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216
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Liu L, Li X, Liu S, Min J, Liu W, Pan X, Fang B, Hu M, Liu Z, Li Y, Zhang H. Identification of QTLs associated with the anaerobic germination potential using a set of Oryza nivara introgression lines. Genes Genomics 2021; 43:399-406. [PMID: 33609225 DOI: 10.1007/s13258-021-01063-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 02/09/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND Rice (Oryza sativa L.) is an important crop and a staple food for half of the population around the world. The recent water and labor shortages are encouraging farmers to shift from traditional transplanting to direct-seeding. However, poor germination and slow elongation of the coleoptile constrains large-scale application of direct-seeding. OBJECTIVE This study was aimed to investigate the genetic basis of the anaerobic germination (AG) potential using a set of Oryza nivara (O. nivara) introgression lines (ILs). METHODS In this study, a total of 131 ILs were developed by introducing O. nivara chromosome segments into the elite indica rice variety 93-11 through advanced backcrossing and repeated selfing. A high-density genetic map has been previously constructed with 1,070 bin-markers. The seeds of ILs were germinated and used to measure coleoptile length under normal and anaerobic conditions. QTLs associated with AG potential were determined in rice. RESULTS Based on the high-density genetic map of the IL population, two QTLs, qAGP1 and qAGP3 associated with AG tolerance were characterized and located on chromosomes 1 and 3, respectively. Each QTL explained 15% of the phenotypic variance. Specifically, the O. nivara-derived chromosome segments of the two QTLs were positively tolerance to anaerobic condition by increasing coleoptile length. In a further analysis of public transcriptome data, a total of 26 and 36 genes within qAGP1 and qAGP3 were transcriptionally induced by anaerobic stress, respectively. CONCLUSIONS Utilization of O. nivara-derived alleles at qAGP1 and qAGP3 can potentially enhance tolerance to anaerobic stress at the germination stage in rice, thereby accelerating breeding of rice varieties to be more adaptative for direct-seeding.
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Affiliation(s)
- Licheng Liu
- College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
- Hunan Rice Research Institute, Hunan Academy of Agricultural Science, Changsha, 410125, China
- MOA Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Changsha, 410125, China
| | - Xiaoxiang Li
- Hunan Rice Research Institute, Hunan Academy of Agricultural Science, Changsha, 410125, China
- MOA Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Changsha, 410125, China
| | - Sanxiong Liu
- Hunan Rice Research Institute, Hunan Academy of Agricultural Science, Changsha, 410125, China
- MOA Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Changsha, 410125, China
| | - Jun Min
- Hunan Rice Research Institute, Hunan Academy of Agricultural Science, Changsha, 410125, China
- MOA Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Changsha, 410125, China
| | - Wenqiang Liu
- Hunan Rice Research Institute, Hunan Academy of Agricultural Science, Changsha, 410125, China
- MOA Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Changsha, 410125, China
| | - Xiaowu Pan
- Hunan Rice Research Institute, Hunan Academy of Agricultural Science, Changsha, 410125, China
- MOA Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Changsha, 410125, China
| | - Baohua Fang
- Hunan Rice Research Institute, Hunan Academy of Agricultural Science, Changsha, 410125, China
- MOA Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Changsha, 410125, China
| | - Min Hu
- Hunan Rice Research Institute, Hunan Academy of Agricultural Science, Changsha, 410125, China
- MOA Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Changsha, 410125, China
| | - Zhongqi Liu
- College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Yongchao Li
- Hunan Rice Research Institute, Hunan Academy of Agricultural Science, Changsha, 410125, China.
- MOA Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Changsha, 410125, China.
| | - Haiqing Zhang
- College of Agriculture, Hunan Agricultural University, Changsha, 410128, China.
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217
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Pina A, Irisarri P, Errea P, Zhebentyayeva T. Mapping Quantitative Trait Loci Associated With Graft (In)Compatibility in Apricot ( Prunus armeniaca L.). FRONTIERS IN PLANT SCIENCE 2021; 12:622906. [PMID: 33679836 PMCID: PMC7933020 DOI: 10.3389/fpls.2021.622906] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/08/2021] [Indexed: 05/29/2023]
Abstract
Graft incompatibility (GI) between the most popular Prunus rootstocks and apricot cultivars is one of the major problems for rootstock usage and improvement. Failure in producing long-leaving healthy grafts greatly affects the range of available Prunus rootstocks for apricot cultivation. Despite recent advances related to the molecular mechanisms of a graft-union formation between rootstock and scion, information on genetic control of this trait in woody plants is essentially missing because of a lack of hybrid crosses, segregating for the trait. In this study, we have employed the next-generation sequencing technology to generate the single-nucleotide polymorphism (SNP) markers and construct parental linkage maps for an apricot F1 population "Moniqui (Mo)" × "Paviot (Pa)" segregating for ability to form successful grafts with universal Prunus rootstock "Marianna 2624". To localize genomic regions associated with this trait, we genotyped 138 individuals from the "Mo × Pa" cross and constructed medium-saturated genetic maps. The female "Mo" and male "Pa" maps were composed of 557 and 501 SNPs and organized in eight linkage groups that covered 780.2 and 690.4 cM of genetic distance, respectively. Parental maps were aligned to the Prunus persica v2.0 genome and revealed a high colinearity with the Prunus reference map. Two-year phenotypic data for characters associated with unsuccessful grafting such as necrotic line (NL), bark and wood discontinuities (BD and WD), and an overall estimate of graft (in)compatibility (GI) were collected for mapping quantitative trait loci (QTLs) on both parental maps. On the map of the graft-compatible parent "Pa", two genomic regions on LG5 (44.9-60.8 cM) and LG8 (33.2-39.2 cM) were associated with graft (in)compatibility characters at different significance level, depending on phenotypic dataset. Of these, the LG8 QTL interval was most consistent between the years and supported by two significant and two putative QTLs. To our best knowledge, this is the first report on QTLs for graft (in)compatibility in woody plants. Results of this work will provide a valuable genomic resource for apricot breeding programs and facilitate future efforts focused on candidate genes discovery for graft (in)compatibility in apricot and other Prunus species.
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Affiliation(s)
- Ana Pina
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Zaragoza, Spain
- Instituto Agroalimentario de Aragón – IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | - Patricia Irisarri
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Zaragoza, Spain
- Instituto Agroalimentario de Aragón – IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | - Pilar Errea
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Zaragoza, Spain
- Instituto Agroalimentario de Aragón – IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | - Tetyana Zhebentyayeva
- The Schatz Center for Tree Molecular Genetics, Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, United States
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218
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Genetic Association Analysis for Relative Growths of Body Compositions and Metabolic Traits to Body Weights in Broilers. Animals (Basel) 2021; 11:ani11020469. [PMID: 33578694 PMCID: PMC7916405 DOI: 10.3390/ani11020469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/03/2021] [Accepted: 02/06/2021] [Indexed: 12/17/2022] Open
Abstract
Simple Summary The relative growth of body components and metabolic traits relative to body weights are phenotypically characterized using joint allometric scaling models, and random regression models (RRMs) are constructed to map quantitative trait loci (QTLs) for allometries of body compositions and metabolic traits in broilers. Prior to statistically inferring the QTLs for the allometric scalings, the QTL candidates in RRMs are obtained by rapidly shrinking most of marker genetic effects to zero with the LASSO technique. Referred to as real joint allometric scaling models, statistical utility of the so-called LASSO-RRM mapping method is demonstrated by computer simulation analysis. Using the F2 population by crossing broiler × Fayoumi, we formulate optimal joint allometric scaling models of fat, shank weight (shank-w) and liver as well as thyroxine (T4) and glucose (GLC) to body weights. For body compositions, a total of 9 QTLs, including 4 additive and 5 dominant, were detected to control the allometric scalings of fat, shank-w and liver to body weights; while for metabolic traits, total 10 QTLs, were mapped to govern the allometries of T4 and GLC to body weights, among which 6 QTLs were of dominant genetic effect. The detected QTLs or highly linked markers can be used to regulate relative growths for meat quality traits to body weight in marker-assisted breeding of broilers. Abstract In animal breeding, body components and metabolic traits always fall behind body weights in genetic improvement, which leads to the decline in standards and qualities of animal products. Phenotypically, the relative growth of multiple body components and metabolic traits relative to body weights are characterized by using joint allometric scaling models, and then random regression models (RRMs) are constructed to map quantitative trait loci (QTLs) for relative grwoth allometries of body compositions and metabolic traits in chicken. Referred to as real joint allometric scaling models, statistical utility of the so-called LASSO-RRM mapping method is given a demonstration by computer simulation analysis. Using the F2 population by crossing broiler × Fayoumi, we formulated optimal joint allometric scaling models of fat, shank weight (shank-w) and liver as well as thyroxine (T4) and glucose (GLC) to body weights. For body compositions, a total of 9 QTLs, including 4 additive and 5 dominant QTLs, were detected to control the allometric scalings of fat, shank-w, and liver to body weights; while a total of 10 QTLs of which 6 were dominant, were mapped to govern the allometries of T4 and GLC to body weights. We characterized relative growths of body compositions and metabolic traits to body weights in broilers with joint allometric scaling models and detected QTLs for the allometry scalings of the relative growths by using RRMs. The identified QTLs, including their highly linked genetic markers, could be used to order relative growths of the body components or metabolic traits to body weights in marker-assisted breeding programs for improving the standard and quality of broiler meat products.
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219
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Govindarajulu R, Hostetler AN, Xiao Y, Chaluvadi SR, Mauro-Herrera M, Siddoway ML, Whipple C, Bennetzen JL, Devos KM, Doust AN, Hawkins JS. Integration of high-density genetic mapping with transcriptome analysis uncovers numerous agronomic QTL and reveals candidate genes for the control of tillering in sorghum. G3-GENES GENOMES GENETICS 2021; 11:6128573. [PMID: 33712819 PMCID: PMC8022972 DOI: 10.1093/g3journal/jkab024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/12/2021] [Indexed: 12/13/2022]
Abstract
Phenotypes such as branching, photoperiod sensitivity, and height were modified during plant domestication and crop improvement. Here, we perform quantitative trait locus (QTL) mapping of these and other agronomic traits in a recombinant inbred line (RIL) population derived from an interspecific cross between Sorghum propinquum and Sorghum bicolor inbred Tx7000. Using low-coverage Illumina sequencing and a bin-mapping approach, we generated ∼1920 bin markers spanning ∼875 cM. Phenotyping data were collected and analyzed from two field locations and one greenhouse experiment for six agronomic traits, thereby identifying a total of 30 QTL. Many of these QTL were penetrant across environments and co-mapped with major QTL identified in other studies. Other QTL uncovered new genomic regions associated with these traits, and some of these were environment-specific in their action. To further dissect the genetic underpinnings of tillering, we complemented QTL analysis with transcriptomics, identifying 6189 genes that were differentially expressed during tiller bud elongation. We identified genes such as Dormancy Associated Protein 1 (DRM1) in addition to various transcription factors that are differentially expressed in comparisons of dormant to elongating tiller buds and lie within tillering QTL, suggesting that these genes are key regulators of tiller elongation in sorghum. Our study demonstrates the usefulness of this RIL population in detecting domestication and improvement-associated genes in sorghum, thus providing a valuable resource for genetic investigation and improvement to the sorghum community.
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Affiliation(s)
| | - Ashley N Hostetler
- Department of Biology, West Virginia University, Morgantown, WV 26505, USA
| | - Yuguo Xiao
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | | | - Margarita Mauro-Herrera
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, OK 74078, USA
| | - Muriel L Siddoway
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Clinton Whipple
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | | | - Katrien M Devos
- Department of Crop and Soil Sciences (Institute for Plant Breeding, Genetics and Genomics), and Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Andrew N Doust
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, OK 74078, USA
| | - Jennifer S Hawkins
- Department of Biology, West Virginia University, Morgantown, WV 26505, USA
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220
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Tran Q, Broman KW. Treatment of the X chromosome in mapping multiple quantitative trait loci. G3-GENES GENOMES GENETICS 2021; 11:6114461. [PMID: 33604671 PMCID: PMC8022961 DOI: 10.1093/g3journal/jkab005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 12/20/2020] [Indexed: 11/25/2022]
Abstract
Statistical methods to map quantitative trait loci (QTL) often neglect the X chromosome and may focus exclusively on autosomal loci. But the X chromosome often requires special treatment: sex and cross-direction covariates may need to be included to avoid spurious evidence of linkage, and the X chromosome may require a separate significance threshold. In multiple-QTL analyses, including the consideration of epistatic interactions, the X chromosome also requires special care and consideration. We extend a penalized likelihood method for multiple-QTL model selection, to appropriately handle the X chromosome. We examine its performance in simulation and by application to a large eQTL data set. The method has been implemented in the package R/qtl.
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Affiliation(s)
- Quoc Tran
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Karl W Broman
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
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221
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Boazak EM, King R, Wang J, Chu CM, Toporek AM, Sherwood JM, Overby DR, Geisert EE, Ethier CR. Smarce1 and Tensin 4 Are Putative Modulators of Corneoscleral Stiffness. Front Bioeng Biotechnol 2021; 9:596154. [PMID: 33634081 PMCID: PMC7902041 DOI: 10.3389/fbioe.2021.596154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/14/2021] [Indexed: 11/13/2022] Open
Abstract
The biomechanical properties of the cornea and sclera are important in the onset and progression of multiple ocular pathologies and vary substantially between individuals, yet the source of this variation remains unknown. Here we identify genes putatively regulating corneoscleral biomechanical tissue properties by conducting high-fidelity ocular compliance measurements across the BXD recombinant inbred mouse set and performing quantitative trait analysis. We find seven cis-eQTLs and non-synonymous SNPs associating with ocular compliance, and show by RT-qPCR and immunolabeling that only two of the candidate genes, Smarce1 and Tns4, showed significant expression in corneal and scleral tissues. Both have mechanistic potential to influence the development and/or regulation of tissue material properties. This work motivates further study of Smarce1 and Tns4 for their role(s) in ocular pathology involving the corneoscleral envelope as well as the development of novel mouse models of ocular pathophysiology, such as myopia and glaucoma.
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Affiliation(s)
- Elizabeth M Boazak
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Emory University, Atlanta, GA, United States
| | - Rebecca King
- Department of Ophthalmology, Emory University, Atlanta, GA, United States
| | - Jiaxing Wang
- Department of Ophthalmology, Emory University, Atlanta, GA, United States
| | - Cassandra M Chu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Emory University, Atlanta, GA, United States
| | - Aaron M Toporek
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Emory University, Atlanta, GA, United States
| | - Joseph M Sherwood
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Darryl R Overby
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Eldon E Geisert
- Department of Ophthalmology, Emory University, Atlanta, GA, United States
| | - C Ross Ethier
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Emory University, Atlanta, GA, United States.,George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, United States
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222
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Talukder ZI, Underwood W, Misar CG, Seiler GJ, Liu Y, Li X, Cai X, Qi L. Unraveling the Sclerotinia Basal Stalk Rot Resistance Derived From Wild Helianthus argophyllus Using a High-Density Single Nucleotide Polymorphism Linkage Map. FRONTIERS IN PLANT SCIENCE 2021; 11:617920. [PMID: 33613588 PMCID: PMC7886805 DOI: 10.3389/fpls.2020.617920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/21/2020] [Indexed: 05/30/2023]
Abstract
Basal stalk rot (BSR), caused by the fungus Sclerotinia sclerotiorum, is a serious disease of sunflower (Helianthus annuus L.) in the humid temperate growing areas of the world. BSR resistance is quantitative and conditioned by multiple genes. Our objective was to dissect the BSR resistance introduced from the wild annual species Helianthus argophyllus using a quantitative trait loci (QTL) mapping approach. An advanced backcross population (AB-QTL) with 134 lines derived from the cross of HA 89 with a H. argophyllus Torr. and Gray accession, PI 494573, was evaluated for BSR resistance in three field and one greenhouse growing seasons of 2017-2019. Highly significant genetic variations (p < 0.001) were observed for BSR disease incidence (DI) in all field screening tests and disease rating and area under the disease progress curve in the greenhouse. The AB-QTL population and its parental lines were genotyped using the genotyping-by-sequencing method. A genetic linkage map spanning 2,045.14 cM was constructed using 3,110 SNP markers mapped on 17 sunflower chromosomes. A total of 21 QTL associated with BSR resistance were detected on 11 chromosomes, each explaining a phenotypic variation ranging from 4.5 to 22.6%. Of the 21 QTL, eight were detected for BSR DI measured in the field, seven were detected for traits measured in the greenhouse, and six were detected from both field and greenhouse tests. Thirteen of the 21 QTL had favorable alleles from the H. argophyllus parent conferring increased BSR resistance.
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Affiliation(s)
- Zahirul I. Talukder
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - William Underwood
- United States Department of Agriculture – Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Christopher G. Misar
- United States Department of Agriculture – Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Gerald J. Seiler
- United States Department of Agriculture – Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Yuan Liu
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Xuehui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Xiwen Cai
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Lili Qi
- United States Department of Agriculture – Agricultural Research Service, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
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223
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Gimode W, Bao K, Fei Z, McGregor C. QTL associated with gummy stem blight resistance in watermelon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:573-584. [PMID: 33135096 PMCID: PMC7843542 DOI: 10.1007/s00122-020-03715-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/23/2020] [Indexed: 05/20/2023]
Abstract
We identified QTLs associated with gummy stem blight resistance in an interspecific F2:3 Citrullus population and developed marker assays for selection of the loci in watermelon. Gummy stem blight (GSB), caused by three Stagonosporopsis spp., is a devastating fungal disease of watermelon (Citrullus lanatus) and other cucurbits that can lead to severe yield losses. Currently, no commercial cultivars with genetic resistance to GSB in the field have been reported. Utilizing GSB-resistant cultivars would reduce yield losses, decrease the high cost of disease control, and diminish hazards resulting from frequent fungicide application. The objective of this study was to identify quantitative trait loci (QTLs) associated with GSB resistance in an F2:3 interspecific Citrullus mapping population (N = 178), derived from a cross between Crimson Sweet (C. lanatus) and GSB-resistant PI 482276 (C. amarus). The population was phenotyped by inoculating seedlings with Stagonosporopsis citrulli 12178A in the greenhouse in two separate experiments, each with three replications. We identified three QTLs (ClGSB3.1, ClGSB5.1 and ClGSB7.1) associated with GSB resistance, explaining between 6.4 and 21.1% of the phenotypic variation. The genes underlying ClGSB5.1 includes an NBS-LRR gene (ClCG05G019540) previously identified as a candidate gene for GSB resistance in watermelon. Locus ClGSB7.1 accounted for the highest phenotypic variation and harbors twenty-two candidate genes associated with disease resistance. Among them is ClCG07G013230, encoding an Avr9/Cf-9 rapidly elicited disease resistance protein, which contains a non-synonymous point mutation in the DUF761 domain that was significantly associated with GSB resistance. High throughput markers were developed for selection of ClGSB5.1 and ClGSB7.1. Our findings will facilitate the use of molecular markers for efficient introgression of the resistance loci and development of GSB-resistant watermelon cultivars.
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Affiliation(s)
- Winnie Gimode
- Institute for Plant Breeding, Genetics & Genomics, University of Georgia, 1111 Plant Sciences Bldg, Athens, GA, 30602, USA
| | - Kan Bao
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA
| | - Cecilia McGregor
- Department of Horticulture and Institute for Plant Breeding, Genetics & Genomics, University of Georgia, 1111 Plant Sciences Bldg, Athens, GA, 30602, USA.
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224
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Liu M, He W, Zhang A, Zhang L, Sun D, Gao Y, Ni P, Ma X, Cui Z, Ruan Y. Genetic analysis of maize shank length by QTL mapping in three recombinant inbred line populations. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 303:110767. [PMID: 33487352 DOI: 10.1016/j.plantsci.2020.110767] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/12/2020] [Accepted: 11/17/2020] [Indexed: 06/12/2023]
Abstract
In maize, the shank is a unique tissue linking the stem to the ear. Shank length (SL) mainly affects the transport of photosynthetic products to the ear and the dehydration of kernels via regulated husk morphology. The limited studies on SL revealed it is a highly heritable quantitative trait controlled by significant additive and additive-dominance effects. However, the genetic basis of SL remains unclear. In this study, we analyzed three maize recombinant inbred line (RIL) populations to elucidate the molecular mechanism underlying the SL. The data indicated the SL varied among the three RIL populations and was highly heritable. Additionally, the SL was positively correlated with the husk length (HL), husk number (HN), ear length (EL), and ear weight (EW) in the BY815/K22 (BYK) and CI7/K22 (CIK) RIL populations, but was negatively correlated with the husk width (HW) in the BYK RIL population. Moreover, 10 quantitative trait loci (QTL) for SL were identified in the three RIL populations, five of which were large-effect QTL. The percentage of the total phenotypic variation explained by the QTL for SL was 13.67 %, 20.45 %, and 30.81 % in the BY815/DE3 (BYD), BYK, and CIK RIL populations, respectively. Further analyses uncovered some genetic overlap between SL and EL, SL and ear row number (ERN), SL and cob weight (CW), and SL and HN. Unlike the large-effect QTL qSL BYK-2-2, which spanned the centromere, the other four large-effect QTL were delimited to a single peak bin via bin map. Furthermore, 2, 5, 6, and 12 genes associated with SL were identified for qSL BYK-2-1, qSL CIK-2-1, qSL CIK-9-1, and qSL CIK-9-2, respectively. Five of the candidate genes for SL may contribute to the hormone metabolism and sphingolipid biosynthesis regulating cell elongation, division, differentiation, and expansion. These results may be relevant for future studies on the genetic basis of SL and for the molecular breeding of maize based on marker-assisted selection to develop new varieties with an ideal SL.
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Affiliation(s)
- Meiling Liu
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China
| | - Wenshu He
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China; Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, Lleida, 25198, Spain
| | - Ao Zhang
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China
| | - Lijun Zhang
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China
| | - Daqiu Sun
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yuan Gao
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China
| | - Pengzun Ni
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xinglin Ma
- Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Zhenhai Cui
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Yanye Ruan
- College of Biological Science and Technology, Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang, 110866, China.
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Xiong P, Hulsey CD, Fruciano C, Wong WY, Nater A, Kautt AF, Simakov O, Pippel M, Kuraku S, Meyer A, Franchini P. The comparative genomic landscape of adaptive radiation in crater lake cichlid fishes. Mol Ecol 2021; 30:955-972. [PMID: 33305470 PMCID: PMC8607476 DOI: 10.1111/mec.15774] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 11/21/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022]
Abstract
Factors ranging from ecological opportunity to genome composition might explain why only some lineages form adaptive radiations. While being rare, particular systems can provide natural experiments within an identical ecological setting where species numbers and phenotypic divergence in two closely related lineages are notably different. We investigated one such natural experiment using two de novo assembled and 40 resequenced genomes and asked why two closely related Neotropical cichlid fish lineages, the Amphilophus citrinellus species complex (Midas cichlids; radiating) and Archocentrus centrarchus (Flyer cichlid; nonradiating), have resulted in such disparate evolutionary outcomes. Although both lineages inhabit many of the same Nicaraguan lakes, whole-genome inferred demography suggests that priority effects are not likely to be the cause of the dissimilarities. Also, genome-wide levels of selection, transposable element dynamics, gene family expansion, major chromosomal rearrangements and the number of genes under positive selection were not markedly different between the two lineages. To more finely investigate particular subsets of the genome that have undergone adaptive divergence in Midas cichlids, we also examined if there was evidence for 'molecular pre-adaptation' in regions identified by QTL mapping of repeatedly diverging adaptive traits. Although most of our analyses failed to pinpoint substantial genomic differences, we did identify functional categories containing many genes under positive selection that provide candidates for future studies on the propensity of Midas cichlids to radiate. Our results point to a disproportionate role of local, rather than genome-wide factors underlying the propensity for these cichlid fishes to adaptively radiate.
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Affiliation(s)
- Peiwen Xiong
- Department of BiologyUniversity of KonstanzKonstanzGermany
| | - C. Darrin Hulsey
- Department of BiologyUniversity of KonstanzKonstanzGermany
- School of Biology and Environmental ScienceUniversity College DublinDublinIreland
| | - Carmelo Fruciano
- Department of BiologyUniversity of KonstanzKonstanzGermany
- National Research Council (CNR) – IRBIMMessinaItaly
| | - Wai Y. Wong
- Department of Molecular Evolution and DevelopmentUniversity of ViennaViennaAustria
| | | | - Andreas F. Kautt
- Department of BiologyUniversity of KonstanzKonstanzGermany
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMAUSA
| | - Oleg Simakov
- Department of Molecular Evolution and DevelopmentUniversity of ViennaViennaAustria
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
| | - Shigehiro Kuraku
- Laboratory for PhyloinformaticsRIKEN Center for Biosystems Dynamics Research (BDR)KobeJapan
| | - Axel Meyer
- Department of BiologyUniversity of KonstanzKonstanzGermany
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226
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Thompson KA, Urquhart-Cronish M, Whitney KD, Rieseberg LH, Schluter D. Patterns, Predictors, and Consequences of Dominance in Hybrids. Am Nat 2021; 197:E72-E88. [PMID: 33625966 DOI: 10.1086/712603] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractCompared to those of their parents, are the traits of first-generation (F1) hybrids typically intermediate, biased toward one parent, or mismatched for alternative parental phenotypes? To address this empirical gap, we compiled data from 233 crosses in which traits were measured in a common environment for two parent taxa and their F1 hybrids. We find that individual traits in F1s are halfway between the parental midpoint and one parental value. Considering pairs of traits together, a hybrid's bivariate phenotype tends to resemble one parent (parent bias) about 50% more than the other, while also exhibiting a similar magnitude of mismatch due to different traits having dominance in conflicting directions. Using data from an experimental field planting of recombinant hybrid sunflowers, we illustrate that parent bias improves fitness, whereas mismatch reduces fitness. Our study has three major conclusions. First, hybrids are not phenotypically intermediate but rather exhibit substantial mismatch. Second, dominance is likely determined by the idiosyncratic evolutionary trajectories of individual traits and populations. Finally, selection against hybrids likely results from selection against both intermediate and mismatched phenotypes.
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227
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Hypothalamic Norepinephrine Concentration and Heart Mass in Hypertensive ISIAH Rats Are Associated with a Genetic Locus on Chromosome 18. J Pers Med 2021; 11:jpm11020067. [PMID: 33498741 PMCID: PMC7911892 DOI: 10.3390/jpm11020067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 12/23/2022] Open
Abstract
The relationship between activation of the sympathetic nervous system and cardiac hypertrophy has long been known. However, the molecular genetic basis of this association is poorly understood. Given the known role of hypothalamic norepinephrine in the activation of the sympathetic nervous system, the aim of the work was to carry out genetic mapping using Quantitative Trait Loci (QTL) analysis and determine the loci associated both with an increase in the concentration of norepinephrine in the hypothalamus and with an increase in heart mass in Inherited Stress-Induced Arterial Hypertension (ISIAH) rats simulating the stress-sensitive form of arterial hypertension. The work describes a genetic locus on chromosome 18, in which there are genes that control the development of cardiac hypertrophy associated with an increase in the concentration of norepinephrine in the hypothalamus, i.e., genes involved in enhanced sympathetic myocardial stimulation. No association of this locus with the blood pressure was found. Taking into consideration previously obtained results, it was concluded that the contribution to the development of heart hypertrophy in the ISIAH rats is controlled by different genetic loci, one of which is associated with the concentration of norepinephrine in the hypothalamus (on chromosome 18) and the other is associated with high blood pressure (on chromosome 1). Nucleotide substitutions that may be involved in the formation or absence of association with blood pressure in different rat strains are discussed.
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228
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Brassac J, Muqaddasi QH, Plieske J, Ganal MW, Röder MS. Linkage mapping identifies a non-synonymous mutation in FLOWERING LOCUS T (FT-B1) increasing spikelet number per spike. Sci Rep 2021; 11:1585. [PMID: 33452357 PMCID: PMC7811022 DOI: 10.1038/s41598-020-80473-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/17/2020] [Indexed: 11/21/2022] Open
Abstract
Total spikelet number per spike (TSN) is a major component of spike architecture in wheat (Triticumaestivum L.). A major and consistent quantitative trait locus (QTL) was discovered for TSN in a doubled haploid spring wheat population grown in the field over 4 years. The QTL on chromosome 7B explained up to 20.5% of phenotypic variance. In its physical interval (7B: 6.37–21.67 Mb), the gene FLOWERINGLOCUST (FT-B1) emerged as candidate for the observed effect. In one of the parental lines, FT-B1 carried a non-synonymous substitution on position 19 of the coding sequence. This mutation modifying an aspartic acid (D) into a histidine (H) occurred in a highly conserved position. The mutation was observed with a frequency of ca. 68% in a set of 135 hexaploid wheat varieties and landraces, while it was not found in other plant species. FT-B1 only showed a minor effect on heading and flowering time (FT) which were dominated by a major QTL on chromosome 5A caused by segregation of the vernalization gene VRN-A1. Individuals carrying the FT-B1 allele with amino acid histidine had, on average, a higher number of spikelets (15.1) than individuals with the aspartic acid allele (14.3) independent of their VRN-A1 allele. We show that the effect of TSN is not mainly related to flowering time; however, the duration of pre-anthesis phases may play a major role.
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Affiliation(s)
- Jonathan Brassac
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr 3, 06466, Stadt Seeland OT Gatersleben, Germany.
| | - Quddoos H Muqaddasi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr 3, 06466, Stadt Seeland OT Gatersleben, Germany.,European Wheat Breeding Center, BASF Agricultural Solutions GmbH, Am Schwabeplan 8, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Jörg Plieske
- TraitGenetics GmbH, Am Schwabeplan 1b, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Martin W Ganal
- TraitGenetics GmbH, Am Schwabeplan 1b, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Marion S Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr 3, 06466, Stadt Seeland OT Gatersleben, Germany
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229
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Mapping quantitative trait loci and predicting candidate genes for leaf angle in maize. PLoS One 2021; 16:e0245129. [PMID: 33406127 PMCID: PMC7787474 DOI: 10.1371/journal.pone.0245129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/22/2020] [Indexed: 11/29/2022] Open
Abstract
Leaf angle of maize is a fundamental determinant of plant architecture and an important trait influencing photosynthetic efficiency and crop yields. To broaden our understanding of the genetic mechanisms of leaf angle formation, we constructed a F3:4 recombinant inbred lines (RIL) population to map QTL for leaf angle. The RIL was derived from a cross between a model inbred line (B73) with expanded leaf architecture and an elite inbred line (Zheng58) with compact leaf architecture. A sum of eight QTL were detected on chromosome 1, 2, 3, 4 and 8. Single QTL explained 4.3 to 14.2% of the leaf angle variance. Additionally, some important QTL were confirmed through a heterogeneous inbred family (HIF) approach. Furthermore, twenty-four candidate genes for leaf angle were predicted through whole-genome re-sequencing and expression analysis in qLA02-01and qLA08-01 regions. These results will be helpful to elucidate the genetic mechanism of leaf angle formation in maize and benefit to clone the favorable allele for leaf angle. Besides, this will be helpful to develop the novel maize varieties with ideal plant architecture through marker-assisted selection.
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230
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Valentini N, Portis E, Botta R, Acquadro A, Pavese V, Cavalet Giorsa E, Torello Marinoni D. Mapping the Genetic Regions Responsible for Key Phenology-Related Traits in the European Hazelnut. FRONTIERS IN PLANT SCIENCE 2021; 12:749394. [PMID: 35003153 PMCID: PMC8733624 DOI: 10.3389/fpls.2021.749394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/24/2021] [Indexed: 05/03/2023]
Abstract
An increasing interest in the cultivation of (European) hazelnut (Corylus avellana) is driving a demand to breed cultivars adapted to non-conventional environments, particularly in the context of incipient climate change. Given that plant phenology is so strongly determined by genotype, a rational approach to support these breeding efforts will be to identify quantitative trait loci (QTLs) and the genes underlying the basis for adaptation. The present study was designed to map QTLs for phenology-related traits, such as the timing of both male and female flowering, dichogamy, and the period required for nuts to reach maturity. The analysis took advantage of an existing linkage map developed from a population of F1 progeny bred from the cross "Tonda Gentile delle Langhe" × "Merveille de Bollwiller," consisting in 11 LG. A total of 42 QTL-harboring regions were identified. Overall, 71 QTLs were detected, 49 on the TGdL map and 22 on the MB map; among these, 21 were classified as major; 13 were detected in at least two of the seasons (stable-major QTL). In detail, 20 QTLs were identified as contributing to the time of male flowering, 15 to time of female flowering, 25 to dichogamy, and 11 to time of nut maturity. LG02 was found to harbor 16 QTLs, while 15 QTLs mapped to LG10 and 14 to LG03. Many of the QTLs were clustered with one another. The major cluster was located on TGdL_02 and consisted of mainly major QTLs governing all the analyzed traits. A search of the key genomic regions revealed 22 candidate genes underlying the set of traits being investigated. Many of them have been described in the literature as involved in processes related to flowering, control of dormancy, budburst, the switch from vegetative to reproductive growth, or the morphogenesis of flowers and seeds.
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Li D, Zhou Z, Lu X, Jiang Y, Li G, Li J, Wang H, Chen S, Li X, Würschum T, Reif JC, Xu S, Li M, Liu W. Genetic Dissection of Hybrid Performance and Heterosis for Yield-Related Traits in Maize. FRONTIERS IN PLANT SCIENCE 2021; 12:774478. [PMID: 34917109 PMCID: PMC8670227 DOI: 10.3389/fpls.2021.774478] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/01/2021] [Indexed: 05/14/2023]
Abstract
Heterosis contributes a big proportion to hybrid performance in maize, especially for grain yield. It is attractive to explore the underlying genetic architecture of hybrid performance and heterosis. Considering its complexity, different from former mapping method, we developed a series of linear mixed models incorporating multiple polygenic covariance structures to quantify the contribution of each genetic component (additive, dominance, additive-by-additive, additive-by-dominance, and dominance-by-dominance) to hybrid performance and midparent heterosis variation and to identify significant additive and non-additive (dominance and epistatic) quantitative trait loci (QTL). Here, we developed a North Carolina II population by crossing 339 recombinant inbred lines with two elite lines (Chang7-2 and Mo17), resulting in two populations of hybrids signed as Chang7-2 × recombinant inbred lines and Mo17 × recombinant inbred lines, respectively. The results of a path analysis showed that kernel number per row and hundred grain weight contributed the most to the variation of grain yield. The heritability of midparent heterosis for 10 investigated traits ranged from 0.27 to 0.81. For the 10 traits, 21 main (additive and dominance) QTL for hybrid performance and 17 dominance QTL for midparent heterosis were identified in the pooled hybrid populations with two overlapping QTL. Several of the identified QTL showed pleiotropic effects. Significant epistatic QTL were also identified and were shown to play an important role in ear height variation. Genomic selection was used to assess the influence of QTL on prediction accuracy and to explore the strategy of heterosis utilization in maize breeding. Results showed that treating significant single nucleotide polymorphisms as fixed effects in the linear mixed model could improve the prediction accuracy under prediction schemes 2 and 3. In conclusion, the different analyses all substantiated the different genetic architecture of hybrid performance and midparent heterosis in maize. Dominance contributes the highest proportion to heterosis, especially for grain yield, however, epistasis contributes the highest proportion to hybrid performance of grain yield.
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Affiliation(s)
- Dongdong Li
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zhiqiang Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaohuan Lu
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yong Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland, Germany
| | - Guoliang Li
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Junhui Li
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Haoying Wang
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Shaojiang Chen
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Xinhai Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tobias Würschum
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Jochen C. Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland, Germany
| | - Shizhong Xu
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
- *Correspondence: Wenxin Liu,
| | - Mingshun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Mingshun Li,
| | - Wenxin Liu
- Key Laboratory of Crop Heterosis and Utilization, The Ministry of Education/Key Laboratory of Crop Genetic Improvement, Beijing Municipality/National Maize Improvement Center/College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- Shizhong Xu,
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Asif MA, Garcia M, Tilbrook J, Brien C, Dowling K, Berger B, Schilling RK, Short L, Trittermann C, Gilliham M, Fleury D, Roy SJ, Pearson AS. Identification of salt tolerance QTL in a wheat RIL mapping population using destructive and non-destructive phenotyping. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:131-140. [PMID: 32835651 DOI: 10.1071/fp20167] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Bread wheat (Triticum aestivum L.) is one of the most important food crops, however it is only moderately tolerant to salinity stress. To improve wheat yield under saline conditions, breeding for improved salinity tolerance of wheat is needed. We have identified nine quantitative trail loci (QTL) for different salt tolerance sub-traits in a recombinant inbred line (RIL) population, derived from the bi-parental cross of Excalibur × Kukri. This population was screened for salinity tolerance subtraits using a combination of both destructive and non-destructive phenotyping. Genotyping by sequencing (GBS) was used to construct a high-density genetic linkage map, consisting of 3236 markers, and utilised for mapping QTL. Of the nine mapped QTL, six were detected under salt stress, including QTL for maintenance of shoot growth under salinity (QG(1-5).asl-5A, QG(1-5).asl-7B) sodium accumulation (QNa.asl-2A), chloride accumulation (QCl.asl-2A, QCl.asl-3A) and potassium:sodium ratio (QK:Na.asl-2DS2). Potential candidate genes within these QTL intervals were shortlisted using bioinformatics tools. These findings are expected to facilitate the breeding of new salt tolerant wheat cultivars.
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Affiliation(s)
- Muhammad A Asif
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and School of Agriculture, Food and Wine & Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Melissa Garcia
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and School of Agriculture, Food and Wine & Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia; and ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, The University of Adelaide, PMB1, Glen Osmond, SA 5064, Australia
| | - Joanne Tilbrook
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and School of Agriculture, Food and Wine & Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Chris Brien
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and Australian Plant Phenomics Facility, The Plant Accelerator, The University of Adelaide, SA 5064, Australia; and School of Information Technology and Mathematical Sciences, The University of South Australia, GPO Box 2471, Adelaide, SA 5001, Australia
| | - Kate Dowling
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and Australian Plant Phenomics Facility, The Plant Accelerator, The University of Adelaide, SA 5064, Australia
| | - Bettina Berger
- School of Agriculture, Food and Wine & Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia; and Australian Plant Phenomics Facility, The Plant Accelerator, The University of Adelaide, SA 5064, Australia
| | - Rhiannon K Schilling
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and School of Agriculture, Food and Wine & Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Laura Short
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and School of Agriculture, Food and Wine & Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Christine Trittermann
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and School of Agriculture, Food and Wine & Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Matthew Gilliham
- School of Agriculture, Food and Wine & Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia; and ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Delphine Fleury
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and School of Agriculture, Food and Wine & Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia; and ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, The University of Adelaide, PMB1, Glen Osmond, SA 5064, Australia; and Innolea, 6 chemin de Panedautes, 31700, Mondonville, France
| | - Stuart J Roy
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and School of Agriculture, Food and Wine & Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia; and ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, The University of Adelaide, PMB1, Glen Osmond, SA 5064, Australia; and Corresponding author.
| | - Allison S Pearson
- Australian Centre for Plant Functional Genomics, PMB 1, Glen Osmond, SA 5064, Australia; and School of Agriculture, Food and Wine & Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia; and ARC Centre of Excellence in Plant Energy Biology, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
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Rollar S, Serfling A, Geyer M, Hartl L, Mohler V, Ordon F. QTL mapping of adult plant and seedling resistance to leaf rust (Puccinia triticina Eriks.) in a multiparent advanced generation intercross (MAGIC) wheat population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:37-51. [PMID: 33201290 PMCID: PMC7813716 DOI: 10.1007/s00122-020-03657-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 07/28/2020] [Indexed: 05/22/2023]
Abstract
The Bavarian MAGIC Wheat population, comprising 394 F6:8 recombinant inbred lines was phenotyped for Puccinia triticina resistance in multi-years' field trials at three locations and in a controlled environment seedling test. Simple intervall mapping revealed 19 QTL, corresponding to 11 distinct chromosomal regions. The biotrophic rust fungus Puccinia triticina is one of the most important wheat pathogens with the potential to cause yield losses up to 70%. Growing resistant cultivars is the most cost-effective and environmentally friendly way to encounter this problem. The emergence of leaf rust races being virulent against common resistance genes increases the demand for wheat varieties with novel resistances. In the past decade, the use of complex experimental populations, like multiparent advanced generation intercross (MAGIC) populations, has risen and offers great advantages for mapping resistances. The genetic diversity of multiple parents, which has been recombined over several generations, leads to a broad phenotypic diversity, suitable for high-resolution mapping of quantitative traits. In this study, interval mapping was performed to map quantitative trait loci (QTL) for leaf rust resistance in the Bavarian MAGIC Wheat population, comprising 394 F6:8 recombinant inbred lines (RILs). Phenotypic evaluation of the RILs for adult plant resistance was carried out in field trials at three locations and two years, as well as in a controlled-environment seedling inoculation test. In total, interval mapping revealed 19 QTL, which corresponded to 11 distinct chromosomal regions controlling leaf rust resistance. Six of these regions may represent putative new QTL. Due to the elite parental material, RILs identified to be resistant to leaf rust can be easily introduced in breeding programs.
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Affiliation(s)
- Sandra Rollar
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin Baur‑Straße 27, 06484 Quedlinburg, Germany
| | - Albrecht Serfling
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin Baur‑Straße 27, 06484 Quedlinburg, Germany
| | - Manuel Geyer
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 8, Freising, Germany
| | - Lorenz Hartl
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 8, Freising, Germany
| | - Volker Mohler
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 8, Freising, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin Baur‑Straße 27, 06484 Quedlinburg, Germany
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234
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Roth C, Murray D, Scott A, Fu C, Averette AF, Sun S, Heitman J, Magwene PM. Pleiotropy and epistasis within and between signaling pathways defines the genetic architecture of fungal virulence. PLoS Genet 2021; 17:e1009313. [PMID: 33493169 PMCID: PMC7861560 DOI: 10.1371/journal.pgen.1009313] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 02/04/2021] [Accepted: 12/17/2020] [Indexed: 01/11/2023] Open
Abstract
Cryptococcal disease is estimated to affect nearly a quarter of a million people annually. Environmental isolates of Cryptococcus deneoformans, which make up 15 to 30% of clinical infections in temperate climates such as Europe, vary in their pathogenicity, ranging from benign to hyper-virulent. Key traits that contribute to virulence, such as the production of the pigment melanin, an extracellular polysaccharide capsule, and the ability to grow at human body temperature have been identified, yet little is known about the genetic basis of variation in such traits. Here we investigate the genetic basis of melanization, capsule size, thermal tolerance, oxidative stress resistance, and antifungal drug sensitivity using quantitative trait locus (QTL) mapping in progeny derived from a cross between two divergent C. deneoformans strains. Using a "function-valued" QTL analysis framework that exploits both time-series information and growth differences across multiple environments, we identified QTL for each of these virulence traits and drug susceptibility. For three QTL we identified the underlying genes and nucleotide differences that govern variation in virulence traits. One of these genes, RIC8, which encodes a regulator of cAMP-PKA signaling, contributes to variation in four virulence traits: melanization, capsule size, thermal tolerance, and resistance to oxidative stress. Two major effect QTL for amphotericin B resistance map to the genes SSK1 and SSK2, which encode key components of the HOG pathway, a fungal-specific signal transduction network that orchestrates cellular responses to osmotic and other stresses. We also discovered complex epistatic interactions within and between genes in the HOG and cAMP-PKA pathways that regulate antifungal drug resistance and resistance to oxidative stress. Our findings advance the understanding of virulence traits among diverse lineages of Cryptococcus, and highlight the role of genetic variation in key stress-responsive signaling pathways as a major contributor to phenotypic variation.
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Affiliation(s)
- Cullen Roth
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- University Program in Genetics and Genomics, Duke University, Durham, North Carolina, United States of America
| | - Debra Murray
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Alexandria Scott
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Ci Fu
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Anna F. Averette
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Paul M. Magwene
- Department of Biology, Duke University, Durham, North Carolina, United States of America
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235
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Pandian BA, Varanasi A, Vennapusa AR, Sathishraj R, Lin G, Zhao M, Tunnell M, Tesso T, Liu S, Prasad PVV, Jugulam M. Characterization, Genetic Analyses, and Identification of QTLs Conferring Metabolic Resistance to a 4-Hydroxyphenylpyruvate Dioxygenase Inhibitor in Sorghum ( Sorghum bicolor). FRONTIERS IN PLANT SCIENCE 2020; 11:596581. [PMID: 33362828 PMCID: PMC7756693 DOI: 10.3389/fpls.2020.596581] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/09/2020] [Indexed: 05/24/2023]
Abstract
Postemergence grass weed control continues to be a major challenge in grain sorghum [Sorghum bicolor (L.) Moench], primarily due to lack of herbicide options registered for use in this crop. The development of herbicide-resistant sorghum technology to facilitate broad-spectrum postemergence weed control can be an economical and viable solution. The 4-hydroxyphenylpyruvate dioxygenase-inhibitor herbicides (e.g., mesotrione or tembotrione) can control a broad spectrum of weeds including grasses, which, however, are not registered for postemergence application in sorghum due to crop injury. In this study, we identified two tembotrione-resistant sorghum genotypes (G-200, G-350) and one susceptible genotype (S-1) by screening 317 sorghum lines from a sorghum association panel (SAP). These tembotrione-resistant and tembotrione-susceptible genotypes were evaluated in a tembotrione dose-response [0, 5.75, 11.5, 23, 46, 92 (label recommended dose), 184, 368, and 736 g ai ha-1] assay. Compared with S-1, the genotypes G-200 and G-350 exhibited 10- and seven fold more resistance to tembotrione, respectively. To understand the inheritance of tembotrione-resistant trait, crosses were performed using S-1 and G-200 or G-350 to generate F1 and F2 progeny. The F1 and F2 progeny were assessed for their response to tembotrione treatment. Genetic analyses of the F1 and F2 progeny demonstrated that the tembotrione resistance in G-200 and G-350 is a partially dominant polygenic trait. Furthermore, cytochrome P450 (CYP)-inhibitor assay using malathion and piperonyl butoxide suggested possible CYP-mediated metabolism of tembotrione in G-200 and G-350. Genotype-by-sequencing based quantitative trait loci (QTL) mapping revealed QTLs associated with tembotrione resistance in G-200 and G-350 genotypes. Overall, the genotypes G-200 and G-350 confer a high level of metabolic resistance to tembotrione and controlled by a polygenic trait. There is an enormous potential to introgress the tembotrione resistance into breeding lines to develop agronomically desirable sorghum hybrids.
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Affiliation(s)
| | | | | | | | - Guifang Lin
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Mingxia Zhao
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Madison Tunnell
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Tesfaye Tesso
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - P. V. Vara Prasad
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
- Sustainable Intensification Innovation Lab, Kansas State University, Manhattan, KS, United States
| | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
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Scheben A, Severn-Ellis AA, Patel D, Pradhan A, Rae SJ, Batley J, Edwards D. Linkage mapping and QTL analysis of flowering time using ddRAD sequencing with genotype error correction in Brassica napus. BMC PLANT BIOLOGY 2020; 20:546. [PMID: 33287721 PMCID: PMC7720618 DOI: 10.1186/s12870-020-02756-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 11/25/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND Brassica napus is an important oilseed crop cultivated worldwide. During domestication and breeding of B. napus, flowering time has been a target of selection because of its substantial impact on yield. Here we use double digest restriction-site associated DNA sequencing (ddRAD) to investigate the genetic basis of flowering in B. napus. An F2 mapping population was derived from a cross between an early-flowering spring type and a late-flowering winter type. RESULTS Flowering time in the mapping population differed by up to 25 days between individuals. High genotype error rates persisted after initial quality controls, as suggested by a genotype discordance of ~ 12% between biological sequencing replicates. After genotype error correction, a linkage map spanning 3981.31 cM and compromising 14,630 single nucleotide polymorphisms (SNPs) was constructed. A quantitative trait locus (QTL) on chromosome C2 was detected, covering eight flowering time genes including FLC. CONCLUSIONS These findings demonstrate the effectiveness of the ddRAD approach to sample the B. napus genome. Our results also suggest that ddRAD genotype error rates can be higher than expected in F2 populations. Quality filtering and genotype correction and imputation can substantially reduce these error rates and allow effective linkage mapping and QTL analysis.
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Affiliation(s)
- Armin Scheben
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA
| | - Anita A Severn-Ellis
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Dhwani Patel
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Aneeta Pradhan
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Stephen J Rae
- BASF Agricultural Solutions Belgium NV, BASF Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052, Ghent, Belgium
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, Australia.
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237
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Zhang Q, Su Z, Guo Y, Zhang S, Jiang L, Wu R. Genome-wide association studies of callus differentiation for the desert tree, Populus euphratica. TREE PHYSIOLOGY 2020; 40:1762-1777. [PMID: 32761189 DOI: 10.1093/treephys/tpaa098] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 07/31/2020] [Indexed: 05/22/2023]
Abstract
Callus differentiation is a key developmental process in plant regeneration from cells. A better understanding of the genetic architecture of callus differentiation timing can help improve tissue transformation and the efficiency of artificial propagation. In this study, we investigated genotypic variation in callus differentiation capacity among 297 diverse P. euphratica trees sampled from a natural population. We employed a genome-wide association study (GWAS) of binary and growth-based parameters to identify loci and characterize the genetic architecture and genetic network underlying regulation of callus differentiation in P. euphratica. The results of this GWAS experiment suggested potential associations controlling whether the callus could differentiate and the process of callus differentiation. We identified multiple significant quantitative trait loci (QTLs), including the genes LOG1 and LOG7 and a locus containing WOX1. We reconstructed a genetic network that visualizes how each QTL interacts uniquely with other variants, and several core QTLs were detected that are involved in the degree of callus differentiation, providing potential targets for selection. This study represents one of the first to identify genetic variants affecting callus differentiation in a forest tree. Our results suggest that callus differentiation may be a typical qualitative-quantitative trait controlled by a major gene as well as polygenes across the genome of P. euphratica. This GWAS will help to design more complex and specific molecular tools for systematically manipulating organ regeneration.
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Affiliation(s)
- Qianru Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zhifang Su
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yunqian Guo
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shilong Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Libo Jiang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Rongling Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA 17033, USA
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238
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Uechi L, Jalali M, Wilbur JD, French JL, Jumbe NL, Meaney MJ, Gluckman PD, Karnani N, Sakhanenko NA, Galas DJ. Complex genetic dependencies among growth and neurological phenotypes in healthy children: Towards deciphering developmental mechanisms. PLoS One 2020; 15:e0242684. [PMID: 33270668 PMCID: PMC7714163 DOI: 10.1371/journal.pone.0242684] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/09/2020] [Indexed: 11/18/2022] Open
Abstract
The genetic mechanisms of childhood development in its many facets remain largely undeciphered. In the population of healthy infants studied in the Growing Up in Singapore Towards Healthy Outcomes (GUSTO) program, we have identified a range of dependencies among the observed phenotypes of fetal and early childhood growth, neurological development, and a number of genetic variants. We have quantified these dependencies using our information theory-based methods. The genetic variants show dependencies with single phenotypes as well as pleiotropic effects on more than one phenotype and thereby point to a large number of brain-specific and brain-expressed gene candidates. These dependencies provide a basis for connecting a range of variants with a spectrum of phenotypes (pleiotropy) as well as with each other. A broad survey of known regulatory expression characteristics, and other function-related information from the literature for these sets of candidate genes allowed us to assemble an integrated body of evidence, including a partial regulatory network, that points towards the biological basis of these general dependencies. Notable among the implicated loci are RAB11FIP4 (next to NF1), MTMR7 and PLD5, all highly expressed in the brain; DNMT1 (DNA methyl transferase), highly expressed in the placenta; and PPP1R12B and DMD (dystrophin), known to be important growth and development genes. While we cannot specify and decipher the mechanisms responsible for the phenotypes in this study, a number of connections for further investigation of fetal and early childhood growth and neurological development are indicated. These results and this approach open the door to new explorations of early human development.
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Affiliation(s)
- Lisa Uechi
- Pacific Northwest Research Institute, Seattle, Washington, United States of America
| | - Mahjoubeh Jalali
- Pacific Northwest Research Institute, Seattle, Washington, United States of America
| | - Jayson D. Wilbur
- Metrum Research Group, Tariffville, CT, United States of America
| | | | - N. L. Jumbe
- Pharmactuarials LLC, Mountain View, CA, United States of America
| | - Michael J. Meaney
- Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR) Institute, Toronto, Canada
| | - Peter D. Gluckman
- Centre for Human Evolution, Adaptation and Disease, Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Neerja Karnani
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Brenner Centre for Molecular Medicine, National University of Singapore, Singapore, Singapore
| | - Nikita A. Sakhanenko
- Pacific Northwest Research Institute, Seattle, Washington, United States of America
- * E-mail: (DJG); (NAS)
| | - David J. Galas
- Pacific Northwest Research Institute, Seattle, Washington, United States of America
- * E-mail: (DJG); (NAS)
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Genetic Analysis of Walnut ( Juglans regia L.) Pellicle Pigment Variation Through a Novel, High-Throughput Phenotyping Platform. G3-GENES GENOMES GENETICS 2020; 10:4411-4424. [PMID: 33008832 PMCID: PMC7718756 DOI: 10.1534/g3.120.401580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Walnut pellicle color is a key quality attribute that drives consumer preference and walnut sales. For the first time a high-throughput, computer vision-based phenotyping platform using a custom algorithm to quantitatively score each walnut pellicle in L* a* b* color space was deployed at large-scale. This was compared to traditional qualitative scoring by eye and was used to dissect the genetics of pellicle pigmentation. Progeny from both a bi-parental population of 168 trees (‘Chandler’ × ‘Idaho’) and a genome-wide association (GWAS) with 528 trees of the UC Davis Walnut Improvement Program were analyzed. Color phenotypes were found to have overlapping regions in the ‘Chandler’ genetic map on Chr01 suggesting complex genetic control. In the GWAS population, multiple, small effect QTL across Chr01, Chr07, Chr08, Chr09, Chr10, Chr12 and Chr13 were discovered. Marker trait associations were co-localized with QTL mapping on Chr01, Chr10, Chr14, and Chr16. Putative candidate genes controlling walnut pellicle pigmentation were postulated.
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240
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Zheng K, Yan J, Deng J, Wu W, Wen Y. Modification of Experimental Design and Statistical Method for Mapping Imprinted QTLs Based on Immortalized F2 Population. Front Genet 2020; 11:589047. [PMID: 33329733 PMCID: PMC7714927 DOI: 10.3389/fgene.2020.589047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/29/2020] [Indexed: 11/20/2022] Open
Abstract
Genomic imprinting is an epigenetic phenomenon, which plays important roles in the growth and development of animals and plants. Immortalized F2 (imF2) populations generated by random cross between recombinant inbred (RI) or doubled haploid (DH) lines have been proved to have significant advantages for mapping imprinted quantitative trait loci (iQTLs), and statistical methods for this purpose have been proposed. In this paper, we propose a special type of imF2 population (R-imF2) for iQTL mapping, which is developed by random reciprocal cross between RI/DH lines. We also propose two modified iQTL mapping methods: two-step point mapping (PM-2) and two-step composite point mapping (CPM-2). Simulation studies indicated that: (i) R-imF2 cannot improve the results of iQTL mapping, but the experimental design can probably reduce the workload of population construction; (ii) PM-2 can increase the precision of estimating the position and effects of a single iQTL; and (iii) CPM-2 can precisely map not only iQTLs, but also non-imprinted QTLs. The modified experimental design and statistical methods will facilitate and promote the study of iQTL mapping.
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Affiliation(s)
- Kehui Zheng
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Computer and Information Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiqiang Yan
- College of Computer and Information Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiacong Deng
- School of Ocean and Biochemical Engineering, Fuqing Branch of Fujian Normal University, Fuzhou, China
| | - Weiren Wu
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Weiren Wu,
| | - Yongxian Wen
- College of Computer and Information Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Yongxian Wen,
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241
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Zhang Z, Taylor L, Shommu N, Ghosh S, Reimer R, Panaccione R, Kaur S, Hyun JE, Cai C, Deehan EC, Hotte N, Madsen KL, Raman M. A Diversified Dietary Pattern Is Associated With a Balanced Gut Microbial Composition of Faecalibacterium and Escherichia/Shigella in Patients With Crohn's Disease in Remission. J Crohns Colitis 2020; 14:1547-1557. [PMID: 32343765 DOI: 10.1093/ecco-jcc/jjaa084] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS Crohn's disease [CD] is associated with alterations in gut microbial composition and function. The present controlled-intervention study investigated the relationship between patterns of dietary intake and baseline gut microbiota in CD patients in remission and examined the effects of a dietary intervention in patients consuming a non-diversified diet [NDD]. METHODS Forty outpatients with quiescent CD were recruited in Calgary, Alberta, Canada. Based on 3-day food records, patients consuming a lower plant-based and higher red and processed meat-based diet were assigned to the NDD group [n = 15] and received a 12-week structured dietary intervention; all other patients were assigned to the diversified diet [DD] control group [n = 25] and received conventional management. Faecal microbiota composition, short chain fatty acids [SCFAs] and calprotectin were measured. RESULTS At baseline the NDD and DD groups had a different faecal microbial beta-diversity [p = 0.003, permutational multivariate analysis of variance]. The NDD group had lower Faecalibacterium and higher Escherichia/Shigella relative abundances compared to the DD group [3.3 ± 5.4% vs. 8.5 ± 10.6%; 6.9 ± 12.2% vs. 1.6 ± 4.4%; p ≤ 0.03, analysis of covariance]. These two genera showed a strong negative correlation [rs = -0.60, q = 0.0002]. Faecal butyrate showed a positive correlation with Faecalibacterium [rs = 0.52, q = 0.002], and an inhibitory relationship with Escherichia/Shigella abundance [four-parameter sigmoidal model, R = -0.83; rs = -0.44, q = 0.01], respectively. After the 12 weeks of dietary intervention, no difference in microbial beta-diversity between the two groups was observed [p = 0.43]. The NDD group demonstrated an increase in Faecalibacterium [p < 0.05, generalized estimated equation model], and resembled the DD group at the end of the intervention [p = 0.84, t-test with permutation]. We did not find an association of diet with faecal SCFAs or calprotectin. CONCLUSIONS Dietary patterns are associated with specific gut microbial compositions in CD patients in remission. A diet intervention in patients consuming a NDD modifies gut microbial composition to resemble that seen in patients consuming a DD. These results show that diet is important in shaping the microbial dysbiosis signature in CD towards a balanced community.
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Affiliation(s)
- Zhengxiao Zhang
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Lorian Taylor
- Department of Medicine, University of Calgary, Calgary, AB, Canada
| | - Nusrat Shommu
- Department of Medicine, University of Calgary, Calgary, AB, Canada
| | - Subrata Ghosh
- Institute of Translational Medicine, NIHR Biomedical Research Centre, University of Birmingham and Birmingham University Hospitals, Birmingham, UK
| | - Raylene Reimer
- Faculty of Kinesiology, University of Calgary, Calgary, Canada
| | - Remo Panaccione
- Department of Medicine, University of Calgary, Calgary, AB, Canada
| | - Sandeep Kaur
- Department of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jae Eun Hyun
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Chenxi Cai
- Program for Pregnancy and Postpartum Health, Women and Children's Health Research Institute, University of Alberta, Edmonton, Canada
| | - Edward C Deehan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Canada
| | - Naomi Hotte
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Karen L Madsen
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Maitreyi Raman
- Department of Medicine, University of Calgary, Calgary, AB, Canada
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242
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Becker CA, Aghalari A, Marufuzzaman M, Stone AE. Predicting dairy cattle heat stress using machine learning techniques. J Dairy Sci 2020; 104:501-524. [PMID: 33131806 DOI: 10.3168/jds.2020-18653] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 08/14/2020] [Indexed: 11/19/2022]
Abstract
The objectives of the study were to use a heat stress scoring system to evaluate the severity of heat stress on dairy cows using different heat abatement techniques. The scoring system ranged from 1 to 4, where 1 = no heat stress; 2 = mild heat stress; 3 = severe heat stress; and 4 = moribund. The accuracy of the scoring system was then predicted using 3 machine learning techniques: logistic regression, Gaussian naïve Bayes, and random forest. To predict the accuracy of the scoring system, these techniques used factors including temperature-humidity index, respiration rate, lying time, lying bouts, total steps, drooling, open-mouth breathing, panting, location in shade or sprinklers, somatic cell score, reticulorumen temperature, hygiene body condition score, milk yield, and milk fat and protein percent. Three different treatments, namely, portable shade structure, portable polyvinyl chloride pipe sprinkler system, or control with no heat abatement, were considered, where each treatment was replicated 3 times with 3 second-trimester lactating cows. Results indicate that random forest outperformed the other 2 methods, with respect to both accuracy and precision, in predicting the sprinkler group's score. Both logistic regression and random forest were consistent in predicting scores for control, shade, and combined groups. The mean probability of predicting non-heat-stressed cows was highest for cows in the sprinkler group. Finally, the logistic regression method worked best for predicting heat-stressed cows in control, shade, and combined. The insights gained from these results could aid dairy producers to detect heat stress before it becomes severe, which could decrease the negative effects of heat stress, such as milk loss.
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Affiliation(s)
- C A Becker
- Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State 39762
| | - A Aghalari
- Department of Industrial and Systems Engineering, Mississippi State University, Mississippi State 39762
| | - M Marufuzzaman
- Department of Industrial and Systems Engineering, Mississippi State University, Mississippi State 39762
| | - A E Stone
- Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State 39762.
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243
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Henriksen R, Höglund A, Fogelholm J, Abbey-Lee R, Johnsson M, Dingemanse NJ, Wright D. Intra-Individual Behavioural Variability: A Trait under Genetic Control. Int J Mol Sci 2020; 21:ijms21218069. [PMID: 33138119 PMCID: PMC7663371 DOI: 10.3390/ijms21218069] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 10/15/2020] [Accepted: 10/19/2020] [Indexed: 11/30/2022] Open
Abstract
When individuals are measured more than once in the same context they do not behave in exactly the same way each time. The degree of predictability differs between individuals, with some individuals showing low levels of variation around their behavioural mean while others show high levels of variation. This intra-individual variability in behaviour has received much less attention than between-individual variability in behaviour, and very little is known about the underlying mechanisms that affect this potentially large but understudied component of behavioural variation. In this study, we combine standardized behavioural tests in a chicken intercross to estimate intra-individual behavioural variability with a large-scale genomics analysis to identify genes affecting intra-individual behavioural variability in an avian population. We used a variety of different anxiety-related behavioural phenotypes for this purpose. Our study shows that intra-individual variability in behaviour has a direct genetic basis that is largely unique compared to the genetic architecture for the standard behavioural measures they are based on (at least in the detected quantitative trait locus). We identify six suggestive candidate genes that may underpin differences in intra-individual behavioural variability, with several of these candidates having previously been linked to behaviour and mental health. These findings demonstrate that intra-individual variability in behaviour appears to be a heritable trait in and of itself on which evolution can act.
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Affiliation(s)
- Rie Henriksen
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, 58183 Linköping, Sweden; (A.H.); (R.A.-L.); (M.J.)
- Correspondence: (R.H.); (D.W.)
| | - Andrey Höglund
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, 58183 Linköping, Sweden; (A.H.); (R.A.-L.); (M.J.)
| | - Jesper Fogelholm
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, 58183 Linköping, Sweden; (A.H.); (R.A.-L.); (M.J.)
| | - Robin Abbey-Lee
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, 58183 Linköping, Sweden; (A.H.); (R.A.-L.); (M.J.)
| | - Martin Johnsson
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, 58183 Linköping, Sweden; (A.H.); (R.A.-L.); (M.J.)
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Niels J. Dingemanse
- Ludwig Maximilians University of Munich (LMU), 82152 Munich, Planegg-Martinsried, Germany;
| | - Dominic Wright
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, 58183 Linköping, Sweden; (A.H.); (R.A.-L.); (M.J.)
- Correspondence: (R.H.); (D.W.)
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244
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Zhang W, Boyle K, Brûlé-Babel AL, Fedak G, Gao P, Robleh Djama Z, Polley B, Cuthbert RD, Randhawa HS, Jiang F, Eudes F, Fobert PR. Genetic Characterization of Multiple Components Contributing to Fusarium Head Blight Resistance of FL62R1, a Canadian Bread Wheat Developed Using Systemic Breeding. FRONTIERS IN PLANT SCIENCE 2020; 11:580833. [PMID: 33193525 PMCID: PMC7649146 DOI: 10.3389/fpls.2020.580833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/16/2020] [Indexed: 05/07/2023]
Abstract
Fusarium head blight (FHB) is a devastating fungal disease of small-grain cereals that results in severe yield and quality losses. FHB resistance is controlled by resistance components including incidence, field severity, visual rating index, Fusarium damaged kernels (FDKs), and the accumulation of the mycotoxin deoxynivalenol (DON). Resistance conferred by each of these components is partial and must be combined to achieve resistance sufficient to protect wheat from yield losses. In this study, two biparental mapping populations were analyzed in Canadian FHB nurseries and quantitative trait loci (QTL) mapped for the traits listed above. Nine genomic loci, on 2AS, 2BS, 3BS, 4AS, 4AL, 4BS, 5AS, 5AL, and 5BL, were enriched for the majority of the QTL controlling FHB resistance. The previously validated FHB resistance QTL on 3BS and 5AS affected resistance to severity, FDK, and DON in these populations. The remaining seven genomic loci colocalize with flowering time and/or plant height QTL. The QTL on 4B was a major contributor to all field resistance traits and plant height in the field. QTL on 4AL showed contrasting effects for FHB resistance between Eastern and Western Canada, indicating a local adapted resistance to FHB. In addition, we also found that the 2AS QTL contributed a major effect for DON, and the 2BS for FDK, while the 5AL conferred mainly effect for both FDK/DON. Results presented here provide insight into the genetic architecture underlying these resistant components and insight into how FHB resistance in wheat is controlled by a complex network of interactions between genes controlling flowering time, plant height, local adaption, and FHB resistance components.
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Affiliation(s)
- Wentao Zhang
- Aquatic and Crop Resources Development, National Research Council of Canada, Saskatoon, SK, Canada
| | - Kerry Boyle
- Aquatic and Crop Resources Development, National Research Council of Canada, Saskatoon, SK, Canada
| | | | - George Fedak
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Peng Gao
- Aquatic and Crop Resources Development, National Research Council of Canada, Saskatoon, SK, Canada
| | - Zeinab Robleh Djama
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Aquatic and Crop Resources Development, National Research Council of Canada, Ottawa, ON, Canada
| | - Brittany Polley
- Aquatic and Crop Resources Development, National Research Council of Canada, Saskatoon, SK, Canada
| | - Richard D. Cuthbert
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Harpinder S. Randhawa
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Fengying Jiang
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - François Eudes
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Pierre R. Fobert
- Aquatic and Crop Resources Development, National Research Council of Canada, Saskatoon, SK, Canada
- Aquatic and Crop Resources Development, National Research Council of Canada, Ottawa, ON, Canada
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245
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Radcliffe RA, Dowell R, Odell AT, Richmond PA, Bennett B, Larson C, Kechris K, Saba LM, Rudra P, Wen S. Systems genetics analysis of the LXS recombinant inbred mouse strains:Genetic and molecular insights into acute ethanol tolerance. PLoS One 2020; 15:e0240253. [PMID: 33095786 PMCID: PMC7584226 DOI: 10.1371/journal.pone.0240253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/22/2020] [Indexed: 11/18/2022] Open
Abstract
We have been using the Inbred Long- and Short-Sleep mouse strains (ILS, ISS) and a recombinant inbred panel derived from them, the LXS, to investigate the genetic underpinnings of acute ethanol tolerance which is considered to be a risk factor for alcohol use disorders (AUDs). Here, we have used RNA-seq to examine the transcriptome of whole brain in 40 of the LXS strains 8 hours after a saline or ethanol "pretreatment" as in previous behavioral studies. Approximately 1/3 of the 14,184 expressed genes were significantly heritable and many were unique to the pretreatment. Several thousand cis- and trans-eQTLs were mapped; a portion of these also were unique to pretreatment. Ethanol pretreatment caused differential expression (DE) of 1,230 genes. Gene Ontology (GO) enrichment analysis suggested involvement in numerous biological processes including astrocyte differentiation, histone acetylation, mRNA splicing, and neuron projection development. Genetic correlation analysis identified hundreds of genes that were correlated to the behaviors. GO analysis indicated that these genes are involved in gene expression, chromosome organization, and protein transport, among others. The expression profiles of the DE genes and genes correlated to AFT in the ethanol pretreatment group (AFT-Et) were found to be similar to profiles of HDAC inhibitors. Hdac1, a cis-regulated gene that is located at the peak of a previously mapped QTL for AFT-Et, was correlated to 437 genes, most of which were also correlated to AFT-Et. GO analysis of these genes identified several enriched biological process terms including neuron-neuron synaptic transmission and potassium transport. In summary, the results suggest widespread genetic effects on gene expression, including effects that are pretreatment-specific. A number of candidate genes and biological functions were identified that could be mediating the behavioral responses. The most prominent of these was Hdac1 which may be regulating genes associated with glutamatergic signaling and potassium conductance.
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Affiliation(s)
- Richard A. Radcliffe
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder CO, United States of America
| | - Robin Dowell
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, United States of America
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
- Department of Computer Science, University of Colorado Boulder, Boulder, CO, United States of America
| | - Aaron T. Odell
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, United States of America
| | - Phillip A. Richmond
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, United States of America
| | - Beth Bennett
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Colin Larson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Katerina Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Laura M. Saba
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Pratyaydipta Rudra
- Department of Statistics, Oklahoma State University, Stillwater, OK, United States of America
| | - Shi Wen
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
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246
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First approach to pod dehiscence in faba bean: genetic and histological analyses. Sci Rep 2020; 10:17678. [PMID: 33077797 PMCID: PMC7572390 DOI: 10.1038/s41598-020-74750-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/11/2020] [Indexed: 02/08/2023] Open
Abstract
Pod dehiscence causes important yield losses in cultivated crops and therefore has been a key trait strongly selected against in crop domestication. In spite of the growing knowledge on the genetic basis of dehiscence in different crops, no information is available so far for faba bean. Here we conduct the first comprehensive study for faba bean pod dehiscence by combining, linkage mapping, comparative genomics, QTL analysis and histological examination of mature pods. Mapping of dehiscence-related genes revealed conservation of syntenic blocks among different legumes. Three QTLs were identified in faba bean chromosomes II, IV and VI, although none of them was stable across years. Histological analysis supports the convergent phenotypic evolution previously reported in cereals and related legume species but revealed a more complex pattern in faba bean. Contrary to common bean and soybean, the faba bean dehiscence zone appears to show functional equivalence to that described in crucifers. The lignified wall fiber layer, which is absent in the paucijuga primitive line Vf27, or less lignified and vacuolated in other dehiscent lines, appears to act as the major force triggering pod dehiscence in this species. While our findings, provide new insight into the mechanisms underlying faba bean dehiscence, full understanding of the molecular bases will require further studies combining precise phenotyping with genomic analysis.
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247
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Rehman F, Gong H, Li Z, Zeng S, Yang T, Ai P, Pan L, Huang H, Wang Y. Identification of fruit size associated quantitative trait loci featuring SLAF based high-density linkage map of goji berry (Lycium spp.). BMC PLANT BIOLOGY 2020; 20:474. [PMID: 33059596 PMCID: PMC7565837 DOI: 10.1186/s12870-020-02567-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/22/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Goji (Lycium spp., 2n = 24) is a fruit bearing woody plant popular as a superfood for extensive medicinal and nutritional advantages. Fruit size associated attributes are important for evaluating small-fruited goji berry and plant architecture. The domestication traits are regulated quantitatively in crop plants but few studies have attempted on genomic regions corresponding to fruit traits. RESULTS In this study, we established high-resolution map using specific locus amplified fragment (SLAF) sequencing for de novo SNPs detection based on 305 F1 individuals derived from L. chinense and L. barbarum and performed quantitative trait loci (QTL) analysis of fruit size related traits in goji berry. The genetic map contained 3495 SLAF markers on 12 LGs, spanning 1649.03 cM with 0.47 cM average interval. Female and male parents and F1 individuals` sequencing depth was 111.85-fold and 168.72-fold and 35.80-fold, respectively. The phenotype data were collected for 2 successive years (2018-2019); however, two-year mean data were combined in an extra year (1819). Total 117 QTLs were detected corresponding to multiple traits, of which 78 QTLs in 2 individual years and 36 QTLs in extra year. Six Promising QTLs (qFW10-6.1, qFL10-2.1, qLL10-2.1, qLD10-2.1, qLD12-4.1, qLA10-2.1) were discovered influencing fruit weight, fruit length and leaf related attributes covering an interval ranged from 27.32-71.59 cM on LG10 with peak LOD of 10.48 and 14.6% PVE. Three QTLs targeting fruit sweetness (qFS3-1, qFS5-2) and fruit firmness (qFF10-1) were also identified. Strikingly, various traits QTLs were overlapped on LG10, in particular, qFL10-2.1 was co-located with qLL10-2.1, qLD10-2.1 and qLA10-2.1 among stable QTLs, harbored tightly linked markers, while qLL10-1 was one major QTL with 14.21 highest LOD and 19.3% variance. As LG10 harbored important traits QTLs, we might speculate that it could be hotspot region regulating fruit size and plant architectures. CONCLUSIONS This report highlights the extremely saturated linkage map using SLAF-seq and novel loci contributing fruit size-related attributes in goji berry. Our results will shed light on domestication traits and further strengthen molecular and genetic underpinnings of goji berry; moreover, these findings would better facilitate to assemble the reference genome, determining potential candidate genes and marker-assisted breeding.
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Affiliation(s)
- Fazal Rehman
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiguang Gong
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zhong Li
- Bairuiyuan Company, Yinchuan, 750000, Ningxia, China
| | - Shaohua Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
- GNNU-SCBG Joint Laboratory of Modern Agricultural Technology, College of Life Sciences, Gannan Normal University, Ganzhou, 341000, Jiangxi, China
| | - Tianshun Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Peiyan Ai
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lizhu Pan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Hongwen Huang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Ying Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China.
- GNNU-SCBG Joint Laboratory of Modern Agricultural Technology, College of Life Sciences, Gannan Normal University, Ganzhou, 341000, Jiangxi, China.
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248
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Volante A, Tondelli A, Desiderio F, Abbruscato P, Menin B, Biselli C, Casella L, Singh N, McCouch SR, Tharreau D, Zampieri E, Cattivelli L, Valè G. Genome wide association studies for japonica rice resistance to blast in field and controlled conditions. RICE (NEW YORK, N.Y.) 2020; 13:71. [PMID: 33030605 PMCID: PMC7544789 DOI: 10.1186/s12284-020-00431-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/24/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Rice blast, caused by the fungus Pyricularia oryzae, represents the most damaging fungal disease of rice worldwide. Utilization of rice resistant cultivars represents a practical way to control the disease. Most of the rice varieties cultivated in Europe and several other temperate regions are severely depleted of blast resistance genes, making the identification of resistant sources in genetic background adapted to temperate environments a priority. Given these assumptions, a Genome Wide Association Study (GWAS) for rice blast resistance was undertaken using a panel of 311 temperate/tropical japonica and indica accessions adapted to temperate conditions and genotyped with 37,423 SNP markers. The panel was evaluated for blast resistance in field, under the pressure of the natural blast population, and in growth chamber, using a mixture of three different fungal strains. RESULTS The parallel screening identified 11 accessions showing high levels of resistance in the two conditions, representing potential donors of resistance sources harbored in rice genotypes adapted to temperate conditions. A general higher resistance level was observed in tropical japonica and indica with respect to temperate japonica varieties. The GWAS identified 14 Marker-Traits Associations (MTAs), 8 of which discovered under field conditions and 6 under growth chamber screening. Three MTAs were identified in both conditions; five MTAs were specifically detected under field conditions while three for the growth chamber inoculation. Comparative analysis of physical/genetic positions of the MTAs showed that most of them were positionally-related with cloned or mapped blast resistance genes or with candidate genes whose functions were compatible for conferring pathogen resistance. However, for three MTAs, indicated as BRF10, BRF11-2 and BRGC11-3, no obvious candidate genes or positional relationships with blast resistance QTLs were identified, raising the possibility that they represent new sources of blast resistance. CONCLUSIONS We identified 14 MTAs for blast resistance using both field and growth chamber screenings. A total of 11 accessions showing high levels of resistance in both conditions were discovered. Combinations of loci conferring blast resistance were identified in rice accessions adapted to temperate conditions, thus allowing the genetic dissection of affordable resistances present in the panel. The obtained information will provide useful bases for both resistance breeding and further characterization of the highlighted resistance loci.
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Affiliation(s)
- Andrea Volante
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100, Vercelli, Italy.
- Present Address: CREA Research Centre for Vegetable and Ornamental Crops, Corso Inglesi 508, 18038, Sanremo, IM, Italy.
| | - Alessandro Tondelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Francesca Desiderio
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Pamela Abbruscato
- PTP Science Park, Rice Genomics Unit, via Einstein, 26900, Lodi, Italy
| | - Barbara Menin
- PTP Science Park, Rice Genomics Unit, via Einstein, 26900, Lodi, Italy
- Centre for Sustainable Future Technologies, Istituto Italiano di Tecnologia, Via Livorno 60, 10144, Torino, Italy
| | - Chiara Biselli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Laura Casella
- SA.PI.SE. Coop. Agricola, via G. Mameli 7, 13100, Vercelli, Italy
| | - Namrata Singh
- School of Integrative Plant Sciences, Plant Breeding and Genetics section, Cornell University, Ithaca, New York, 14850, USA
| | - Susan R McCouch
- School of Integrative Plant Sciences, Plant Breeding and Genetics section, Cornell University, Ithaca, New York, 14850, USA
| | - Didier Tharreau
- UMR BGPI, CIRAD, TA A54/K, F 34398, Montpellier, France
- BGPI, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Elisa Zampieri
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100, Vercelli, Italy
- Present Address: Institute for Sustainable Plant Protection, National Research Council, Turin, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Giampiero Valè
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100, Vercelli, Italy.
- Dipartimento di Scienze e Innovazione Tecnologica, Complesso Universitario S. Giuseppe, University of Piemonte Orientale, Piazza S. Eusebio 5, 13100, Vercelli, Italy.
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249
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Linke V, Overmyer KA, Miller IJ, Brademan DR, Hutchins PD, Trujillo EA, Reddy TR, Russell JD, Cushing EM, Schueler KL, Stapleton DS, Rabaglia ME, Keller MP, Gatti DM, Keele GR, Pham D, Broman KW, Churchill GA, Attie AD, Coon JJ. A large-scale genome-lipid association map guides lipid identification. Nat Metab 2020; 2:1149-1162. [PMID: 32958938 PMCID: PMC7572687 DOI: 10.1038/s42255-020-00278-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 08/11/2020] [Indexed: 12/13/2022]
Abstract
Despite the crucial roles of lipids in metabolism, we are still at the early stages of comprehensively annotating lipid species and their genetic basis. Mass spectrometry-based discovery lipidomics offers the potential to globally survey lipids and their relative abundances in various biological samples. To discover the genetics of lipid features obtained through high-resolution liquid chromatography-tandem mass spectrometry, we analysed liver and plasma from 384 diversity outbred mice, and quantified 3,283 molecular features. These features were mapped to 5,622 lipid quantitative trait loci and compiled into a public web resource termed LipidGenie. The data are cross-referenced to the human genome and offer a bridge between genetic associations in humans and mice. Harnessing this resource, we used genome-lipid association data as an additional aid to identify a number of lipids, for example gangliosides through their association with B4galnt1, and found evidence for a group of sex-specific phosphatidylcholines through their shared locus. Finally, LipidGenie's ability to query either mass or gene-centric terms suggests acyl-chain-specific functions for proteins of the ABHD family.
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Affiliation(s)
- Vanessa Linke
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Katherine A Overmyer
- Morgridge Institute for Research, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ian J Miller
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Dain R Brademan
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Paul D Hutchins
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Edna A Trujillo
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Thiru R Reddy
- Morgridge Institute for Research, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Emily M Cushing
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Kathryn L Schueler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Donald S Stapleton
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Mary E Rabaglia
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Mark P Keller
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Duy Pham
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - Karl W Broman
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Alan D Attie
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
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250
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Hofer E, Roshchupkin GV, Adams HHH, Knol MJ, Lin H, Li S, Zare H, Ahmad S, Armstrong NJ, Satizabal CL, Bernard M, Bis JC, Gillespie NA, Luciano M, Mishra A, Scholz M, Teumer A, Xia R, Jian X, Mosley TH, Saba Y, Pirpamer L, Seiler S, Becker JT, Carmichael O, Rotter JI, Psaty BM, Lopez OL, Amin N, van der Lee SJ, Yang Q, Himali JJ, Maillard P, Beiser AS, DeCarli C, Karama S, Lewis L, Harris M, Bastin ME, Deary IJ, Veronica Witte A, Beyer F, Loeffler M, Mather KA, Schofield PR, Thalamuthu A, Kwok JB, Wright MJ, Ames D, Trollor J, Jiang J, Brodaty H, Wen W, Vernooij MW, Hofman A, Uitterlinden AG, Niessen WJ, Wittfeld K, Bülow R, Völker U, Pausova Z, Bruce Pike G, Maingault S, Crivello F, Tzourio C, Amouyel P, Mazoyer B, Neale MC, Franz CE, Lyons MJ, Panizzon MS, Andreassen OA, Dale AM, Logue M, Grasby KL, Jahanshad N, Painter JN, Colodro-Conde L, Bralten J, Hibar DP, Lind PA, Pizzagalli F, Stein JL, Thompson PM, Medland SE, Sachdev PS, Kremen WS, Wardlaw JM, Villringer A, van Duijn CM, Grabe HJ, Longstreth WT, Fornage M, Paus T, Debette S, Ikram MA, Schmidt H, Schmidt R, Seshadri S. Genetic correlations and genome-wide associations of cortical structure in general population samples of 22,824 adults. Nat Commun 2020; 11:4796. [PMID: 32963231 PMCID: PMC7508833 DOI: 10.1038/s41467-020-18367-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 08/20/2020] [Indexed: 12/22/2022] Open
Abstract
Cortical thickness, surface area and volumes vary with age and cognitive function, and in neurological and psychiatric diseases. Here we report heritability, genetic correlations and genome-wide associations of these cortical measures across the whole cortex, and in 34 anatomically predefined regions. Our discovery sample comprises 22,824 individuals from 20 cohorts within the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium and the UK Biobank. We identify genetic heterogeneity between cortical measures and brain regions, and 160 genome-wide significant associations pointing to wnt/β-catenin, TGF-β and sonic hedgehog pathways. There is enrichment for genes involved in anthropometric traits, hindbrain development, vascular and neurodegenerative disease and psychiatric conditions. These data are a rich resource for studies of the biological mechanisms behind cortical development and aging.
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Affiliation(s)
- Edith Hofer
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, Graz, Austria
- Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | - Gennady V Roshchupkin
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Medical Informatics, Erasmus MC, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Hieab H H Adams
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Maria J Knol
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Honghuang Lin
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Shuo Li
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Habil Zare
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, USA
- Department of Cell Systems & Anatomy, The University of Texas Health Science Center, San Antonio, TX, USA
| | - Shahzad Ahmad
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | | | - Claudia L Satizabal
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | | | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, Epidemiology and Health Services, University of Washington, Seattle, WA, USA
| | - Nathan A Gillespie
- Virginia Institute for Psychiatric and Behavior Genetics, Virginia Commonwealth University, Richmond, VA, USA
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Michelle Luciano
- Centre for Cognitive Epidemiology and Cognitive Ageing, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Aniket Mishra
- University of Bordeaux, Bordeaux Population Health Research Center, INSERM UMR 1219, Bordeaux, France
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Rui Xia
- Institute of Molecular Medicine and Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Xueqiu Jian
- Institute of Molecular Medicine and Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Thomas H Mosley
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Yasaman Saba
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Graz, Austria
| | - Lukas Pirpamer
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, Graz, Austria
| | - Stephan Seiler
- Imaging of Dementia and Aging (IDeA) Laboratory, Department of Neurology, University of California-Davis, Davis, CA, USA
- Department of Neurology and Center for Neuroscience, University of California at Davis, Sacramento, CA, USA
| | - James T Becker
- Departments of Psychiatry, Neurology, and Psychology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Pediatrics at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, Epidemiology and Health Services, University of Washington, Seattle, WA, USA
| | - Oscar L Lopez
- Departments of Psychiatry, Neurology, and Psychology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | | | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Jayandra J Himali
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Pauline Maillard
- Imaging of Dementia and Aging (IDeA) Laboratory, Department of Neurology, University of California-Davis, Davis, CA, USA
- Department of Neurology and Center for Neuroscience, University of California at Davis, Sacramento, CA, USA
| | - Alexa S Beiser
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Charles DeCarli
- Imaging of Dementia and Aging (IDeA) Laboratory, Department of Neurology, University of California-Davis, Davis, CA, USA
- Department of Neurology and Center for Neuroscience, University of California at Davis, Sacramento, CA, USA
| | - Sherif Karama
- McGill University, Montreal Neurological Institute, Montreal, QC, Canada
| | - Lindsay Lewis
- McGill University, Montreal Neurological Institute, Montreal, QC, Canada
| | - Mat Harris
- Centre for Cognitive Epidemiology and Cognitive Ageing, University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Brain Research Imaging Centre, University of Edinburgh, Edinburgh, UK
- Scottish Imaging Network, A Platform for Scientific Excellence (SINAPSE) Collaboration, Department of Neuroimaging Sciences, The University of Edinburgh, Edinburgh, UK
| | - Mark E Bastin
- Centre for Cognitive Epidemiology and Cognitive Ageing, University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Brain Research Imaging Centre, University of Edinburgh, Edinburgh, UK
- Scottish Imaging Network, A Platform for Scientific Excellence (SINAPSE) Collaboration, Department of Neuroimaging Sciences, The University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Centre for Cognitive Epidemiology and Cognitive Ageing, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - A Veronica Witte
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Faculty of Medicine, CRC 1052 Obesity Mechanisms, University of Leipzig, Leipzig, Germany
| | - Frauke Beyer
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Faculty of Medicine, CRC 1052 Obesity Mechanisms, University of Leipzig, Leipzig, Germany
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Karen A Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, Australia
- Neuroscience Research Australia, Sydney, Australia
| | - Peter R Schofield
- Neuroscience Research Australia, Sydney, Australia
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Anbupalam Thalamuthu
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, Australia
| | - John B Kwok
- School of Medical Sciences, University of New South Wales, Sydney, Australia
- Brain and Mind Centre - The University of Sydney, Camperdown, NSW, Australia
| | - Margaret J Wright
- Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD, Australia
| | - David Ames
- National Ageing Research Institute, Royal Melbourne Hospital, Parkvill, VIC, Australia
- Academic Unit for Psychiatry of Old Age, University of Melbourne, St George's Hospital, Kew, VIC, Australia
| | - Julian Trollor
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, Australia
- Department of Developmental Disability Neuropsychiatry, School of Psychiatry, University of New South Wales, Sydney, NSW, Australia
| | - Jiyang Jiang
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, Australia
| | - Henry Brodaty
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, Australia
- Dementia Centre for Research Collaboration, University of New South Wales, Sydney, NSW, Australia
| | - Wei Wen
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, Australia
| | - Meike W Vernooij
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Wiro J Niessen
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
- Imaging Physics, Faculty of Applied Sciences, Delft University of Technology, Delft, The Netherlands
| | - Katharina Wittfeld
- German Center for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, Greifswald, Germany
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Robin Bülow
- Institute for Diagnostic Radiology and Neuroradiology, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Zdenka Pausova
- Hospital for Sick Children, Toronto, ON, Canada
- Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, ON, Canada
| | - G Bruce Pike
- Departments of Radiology and Clinial Neurosciences, University of Calgary, Calgary, AB, Canada
| | - Sophie Maingault
- Institut des Maladies Neurodégénratives UMR5293, CEA, CNRS, University of Bordeaux, Bordeaux, France
| | - Fabrice Crivello
- Institut des Maladies Neurodégénratives UMR5293, CEA, CNRS, University of Bordeaux, Bordeaux, France
| | - Christophe Tzourio
- University of Bordeaux, Bordeaux Population Health Research Center, INSERM UMR 1219, Bordeaux, France
- Pole de santé publique, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
| | - Philippe Amouyel
- Centre Hospitalier Universitaire de Bordeaux, France; Inserm U1167, Lille, France
- Department of Epidemiology and Public Health, Pasteur Institute of Lille, Lille, France
- Department of Public Health, Lille University Hospital, Lille, France
| | - Bernard Mazoyer
- Institut des Maladies Neurodégénratives UMR5293, CEA, CNRS, University of Bordeaux, Bordeaux, France
| | - Michael C Neale
- Virginia Institute for Psychiatric and Behavior Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Carol E Franz
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Michael J Lyons
- Department of Psychological and Brain Sciences, Boston University, Boston, MA, USA
| | - Matthew S Panizzon
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Ole A Andreassen
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo and Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Anders M Dale
- Departments of Radiology and Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Mark Logue
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- National Center for PTSD at Boston VA Healthcare System, Boston, MA, USA
- Department of Psychiatry and Department of Medicine-Biomedical Genetics Section, Boston University School of Medicine, Boston, MA, USA
| | - Katrina L Grasby
- Psychiatric Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Neda Jahanshad
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Jodie N Painter
- Psychiatric Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Lucía Colodro-Conde
- Psychiatric Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Janita Bralten
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Derrek P Hibar
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
- Neuroscience Biomarkers, Janssen Research and Development, LLC, San Diego, CA, USA
| | - Penelope A Lind
- Psychiatric Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Fabrizio Pizzagalli
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Jason L Stein
- Department of Genetics & UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Paul M Thompson
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Sarah E Medland
- Psychiatric Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, Australia
- Neuropsychiatric Institute, Prince of Wales Hospital, Sydney, NSW, Australia
| | - William S Kremen
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Joanna M Wardlaw
- Centre for Cognitive Epidemiology and Cognitive Ageing, University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Brain Research Imaging Centre, University of Edinburgh, Edinburgh, UK
- Scottish Imaging Network, A Platform for Scientific Excellence (SINAPSE) Collaboration, Department of Neuroimaging Sciences, The University of Edinburgh, Edinburgh, UK
| | - Arno Villringer
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Day Clinic for Cognitive Neurology, University Hospital Leipzig, Leipzig, Germany
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Hans J Grabe
- German Center for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, Greifswald, Germany
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - William T Longstreth
- Departments of Neurology and Epidemiology, University of Washington, Seattle, WA, USA
| | - Myriam Fornage
- Institute of Molecular Medicine and Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Tomas Paus
- Bloorview Research Institute, Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON, Canada
- Departments of Psychology and Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Stephanie Debette
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- University of Bordeaux, Bordeaux Population Health Research Center, INSERM UMR 1219, Bordeaux, France
- CHU de Bordeaux, Department of Neurology, F-33000, Bordeaux, France
| | - M Arfan Ikram
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
- Department of Neurology, Erasmus MC, Rotterdam, The Netherlands
| | - Helena Schmidt
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Graz, Austria
| | - Reinhold Schmidt
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, Graz, Austria.
| | - Sudha Seshadri
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, USA.
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA.
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