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Priyanatha C, Torkamaneh D, Rajcan I. Genome-Wide Association Study of Soybean Germplasm Derived From Canadian × Chinese Crosses to Mine for Novel Alleles to Improve Seed Yield and Seed Quality Traits. FRONTIERS IN PLANT SCIENCE 2022; 13:866300. [PMID: 35419011 PMCID: PMC8996715 DOI: 10.3389/fpls.2022.866300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/04/2022] [Indexed: 05/16/2023]
Abstract
Genome-wide association study (GWAS) has emerged in the past decade as a viable tool for identifying beneficial alleles from a genomic diversity panel. In an ongoing effort to improve soybean [Glycine max (L.) Merr.], which is the third largest field crop in Canada, a GWAS was conducted to identify novel alleles underlying seed yield and seed quality and agronomic traits. The genomic panel consisted of 200 genotypes including lines derived from several generations of bi-parental crosses between modern Canadian × Chinese cultivars (CD-CH). The genomic diversity panel was field evaluated at two field locations in Ontario in 2019 and 2020. Genotyping-by-sequencing (GBS) was conducted and yielded almost 32 K high-quality SNPs. GWAS was conducted using Fixed and random model Circulating Probability Unification (FarmCPU) model on the following traits: seed yield, seed protein concentration, seed oil concentration, plant height, 100 seed weight, days to maturity, and lodging score that allowed to identify five QTL regions controlling seed yield and seed oil and protein content. A candidate gene search identified a putative gene for each of the three traits. The results of this GWAS study provide insight into potentially valuable genetic resources residing in Chinese modern cultivars that breeders may use to further improve soybean seed yield and seed quality traits.
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Affiliation(s)
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
- *Correspondence: Istvan Rajcan,
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Feitosa-Araujo E, da Fonseca-Pereira P, Knorr LS, Schwarzländer M, Nunes-Nesi A. NAD meets ABA: connecting cellular metabolism and hormone signaling. TRENDS IN PLANT SCIENCE 2022; 27:16-28. [PMID: 34426070 DOI: 10.1016/j.tplants.2021.07.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/04/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
NAD is a ubiquitous metabolic coenzyme. Although the role of NAD as a central redox shuttle remains of critical interest in plant metabolism, recent evidence indicates that NAD serves additional functions in signaling and regulation. A link with the plant stress hormone abscisic acid (ABA) has emerged on the basis of similar plant phenotypes following interference with NAD or ABA, especially in stomatal development, stomatal movements, responses to pathogens and abiotic stress insults, and seed germination. The association between NAD and ABA regulation appears specific and cannot be accounted for by pleiotropic interference. Here, we review the current picture of the NAD - ABA relationship, discuss emerging candidate mechanisms, and assess avenues to dissect interaction mechanisms.
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Affiliation(s)
- Elias Feitosa-Araujo
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-Universität Münster, 48143 Münster, Germany.
| | - Paula da Fonseca-Pereira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Lena S Knorr
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-Universität Münster, 48143 Münster, Germany
| | - Markus Schwarzländer
- Institute of Plant Biology and Biotechnology, Westfälische Wilhelms-Universität Münster, 48143 Münster, Germany
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
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Christie N, Mannapperuma C, Ployet R, van der Merwe K, Mähler N, Delhomme N, Naidoo S, Mizrachi E, Street NR, Myburg AA. qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE). BMC Bioinformatics 2021; 22:595. [PMID: 34911434 PMCID: PMC8672637 DOI: 10.1186/s12859-021-04514-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Affordable high-throughput DNA and RNA sequencing technologies are allowing genomic analysis of plant and animal populations and as a result empowering new systems genetics approaches to study complex traits. The availability of intuitive tools to browse and analyze the resulting large-scale genetic and genomic datasets remain a significant challenge. Furthermore, these integrative genomics approaches require innovative methods to dissect the flow and interconnectedness of biological information underlying complex trait variation. The Plant Genome Integrative Explorer (PlantGenIE.org) is a multi-species database and domain that houses online tools for model and woody plant species including Eucalyptus. Since the Eucalyptus Genome Integrative Explorer (EucGenIE) is integrated within PlantGenIE, it shares genome and expression analysis tools previously implemented within the various subdomains (ConGenIE, PopGenIE and AtGenIE). Despite the success in setting up integrative genomics databases, online tools for systems genetics modelling and high-resolution dissection of complex trait variation in plant populations have been lacking. RESULTS We have developed qtlXplorer ( https://eucgenie.org/QTLXplorer ) for visualizing and exploring systems genetics data from genome-wide association studies including quantitative trait loci (QTLs) and expression-based QTL (eQTL) associations. This module allows users to, for example, find co-located QTLs and eQTLs using an interactive version of Circos, or explore underlying genes using JBrowse. It provides users with a means to build systems genetics models and generate hypotheses from large-scale population genomics data. We also substantially upgraded the EucGenIE resource and show how it enables users to combine genomics and systems genetics approaches to discover candidate genes involved in biotic stress responses and wood formation by focusing on two multigene families, laccases and peroxidases. CONCLUSIONS qtlXplorer adds a new dimension, population genomics, to the EucGenIE and PlantGenIE environment. The resource will be of interest to researchers and molecular breeders working in Eucalyptus and other woody plant species. It provides an example of how systems genetics data can be integrated with functional genetics data to provide biological insight and formulate hypotheses. Importantly, integration within PlantGenIE enables novel comparative genomics analyses to be performed from population-scale data.
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Affiliation(s)
- Nanette Christie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa.
| | - Chanaka Mannapperuma
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 907 81, Umeå, Sweden
| | - Raphael Ployet
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Karen van der Merwe
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Niklas Mähler
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 907 81, Umeå, Sweden
| | - Nicolas Delhomme
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - Sanushka Naidoo
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Nathaniel R Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 907 81, Umeå, Sweden.
| | - Alexander A Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
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104
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Davoodi P, Ehsani A, Vaez Torshizi R, Masoudi AA. New insights into genetics underlying of plumage color. Anim Genet 2021; 53:80-93. [PMID: 34855995 DOI: 10.1111/age.13156] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2021] [Indexed: 01/12/2023]
Abstract
Plumage color can be considered as a social signal in chickens and a breeding identification tool among breeders. The relationship between plumage color and trait groups of immunity, growth and fertility is still a controversial issue. This research aimed to determine the genome-wide additive and epistatic variants affecting plumage color variation in chickens using the chicken Illumina 60k high-density SNP array. Two scenarios of genome-wide additive association studies using all SNPs and independent SNPs were carried out. To perform epistatic association analysis, the LD pruning approach was used to reduce the complexity of the analysis. We detected seven novel significant loci using all of the SNPs in the model and 14 SNPs using the LD pruning approach associated with plumage color. Moreover, 89 significantly associated SNP-SNP interactions (P-value <10-6 ) distributed in 25 chromosomes were identified, indicating that all of the signals together putatively influence the quantitative variation of plumage color. By annotating genes relevant to top SNPs, we have distinguished 18 potential candidate genes comprising HNF4beta, CKMT1B, TBC1D22A, RPL8, CACNA2D1, FZD4, SGMS1, IRF8, OPTN, LOC420362, TRABD, OvoDA1, DAD1, USP6, RBM12B, MIR1772, MIR1709 and MIR6696 and also 89 putative gene-gene combinations responsible for plumage color variation in chickens. Furthermore, several KEGG pathways including metabolic pathway, cytokine-cytokine receptor interaction, focal adhesion, melanogenesis, glycosaminoglycan biosynthesis-keratan sulfate and sphingolipid metabolism were enriched in the gene-set analysis. The results indicated that plumage color is a highly polygenic trait which, in turn, can be affected by multiple coding genes, regulatory genes and gene-gene epistasis interactions. In addition to genes with additive effects, epistatic genes with tiny individual effect sizes but significant effects in a pair have the potential to control plumage coloration in chickens.
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Affiliation(s)
- P Davoodi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, 14115-336, Tehran, Iran
| | - A Ehsani
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, 14115-336, Tehran, Iran
| | - R Vaez Torshizi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, 14115-336, Tehran, Iran
| | - A A Masoudi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, 14115-336, Tehran, Iran
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105
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Expression level is a major modifier of the fitness landscape of a protein coding gene. Nat Ecol Evol 2021; 6:103-115. [PMID: 34795386 DOI: 10.1038/s41559-021-01578-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 10/01/2021] [Indexed: 11/09/2022]
Abstract
The phenotypic consequence of a genetic mutation depends on many factors including the expression level of a gene. However, a comprehensive quantification of this expression effect is still lacking, as is a further general mechanistic understanding of the effect. Here, we measured the fitness effect of almost all (>97.5%) single-nucleotide mutations in GFP, an exogenous gene with no physiological function, and URA3, a conditionally essential gene. Both genes were driven by two promoters whose expression levels differed by around tenfold. The resulting fitness landscapes revealed that the fitness effects of at least 42% of all single-nucleotide mutations within the genes were expression dependent. Although only a small fraction of variation in fitness effects among different mutations can be explained by biophysical properties of the protein and messenger RNA of the gene, our analyses revealed that the avoidance of stochastic molecular errors generally underlies the expression dependency of mutational effects and suggested protein misfolding as the most important type of molecular error among those examined. Our results therefore directly explained the slower evolution of highly expressed genes and highlighted cytotoxicity due to stochastic molecular errors as a non-negligible component for understanding the phenotypic consequence of mutations.
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106
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Zhang X, Luan P, Cao D, Hu G. A High-Density Genetic Linkage Map and Fine Mapping of QTL For Feed Conversion Efficiency in Common Carp ( Cyprinus carpio). Front Genet 2021; 12:778487. [PMID: 34868267 PMCID: PMC8633483 DOI: 10.3389/fgene.2021.778487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/22/2021] [Indexed: 12/02/2022] Open
Abstract
Feed conversion efficiency (FCE) is an economically crucial trait in fish, however, little progress has been made in genetics and genomics for this trait because phenotypes of the trait are difficult to measure. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,416 SNP markers for common carp (Cyprinus carpio) based on high throughput genotyping with the carp 250K single nucleotide polymorphism (SNP) array in a full-sib F1 family of mirror carp (Cyprinus carpio) consisting of 141 progenies. The linkage map contained 11,983 distinct loci and spanned 3,590.09 cM with an average locus interval of 0.33 cM. A total of 17 QTL for the FCE trait were detected on four LGs (LG9, LG20, LG28, and LG32), explaining 8.9-15.9% of the phenotypic variations. One major cluster containing eight QTL (qFCE1-28, qFCE2-28, qFCE3-28, qFCE4-28, qFCE5-28, qFCE6-28, qFCE7-28, and qFCE8-28) was detected on LG28. Two clusters consisting of four QTL (qFCE1-32, qFCE2-32, qFCE3-32, and qFCE4-32) and three QTL (qFCE1-20, qFCE2-20, and qFCE3-20) were detected on LG32 and LG20, respectively. Nine candidate genes (ACACA, SCAF4, SLC2A5, TNMD, PCDH1, FOXO, AGO1, FFAR3, and ARID1A) underlying the feed efficiency trait were also identified, the biological functions of which may be involved in lipid metabolism, carbohydrate metabolism, energy deposition, fat accumulation, digestion, growth regulation, and cell proliferation and differentiation according to GO (Gene Ontology). As an important tool, high-density and high-resolution genetic linkage maps play a crucial role in the QTL fine mapping of economically important traits. Our novel findings provided new insights that elucidate the genetic basis and molecular mechanism of feed efficiency and the subsequent marker-assisted selection breeding in common carp.
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Affiliation(s)
- Xiaofeng Zhang
- National and Local United Engineering Laboratory for Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | | | | | - Guo Hu
- National and Local United Engineering Laboratory for Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
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107
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Habimana R, Ngeno K, Okeno TO, Hirwa CDA, Keambou Tiambo C, Yao NK. Genome-Wide Association Study of Growth Performance and Immune Response to Newcastle Disease Virus of Indigenous Chicken in Rwanda. Front Genet 2021; 12:723980. [PMID: 34745207 PMCID: PMC8570395 DOI: 10.3389/fgene.2021.723980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/15/2021] [Indexed: 11/13/2022] Open
Abstract
A chicken genome has several regions with quantitative trait loci (QTLs). However, replication and confirmation of QTL effects are required particularly in African chicken populations. This study identified single nucleotide polymorphisms (SNPs) and putative genes responsible for body weight (BW) and antibody response (AbR) to Newcastle disease (ND) in Rwanda indigenous chicken (IC) using genome-wide association studies (GWAS). Multiple testing was corrected using chromosomal false detection rates of 5 and 10% for significant and suggestive thresholds, respectively. BioMart data mining and variant effect predictor tools were used to annotate SNPs and candidate genes, respectively. A total of four significant SNPs (rs74098018, rs13792572, rs314702374, and rs14123335) significantly (p ≤ 7.6E-5) associated with BW were identified on chromosomes (CHRs) 8, 11, and 19. In the vicinity of these SNPs, four genes such as pre-B-cell leukaemia homeobox 1 (PBX1), GPATCH1, MPHOSPH6, and MRM1 were identified. Four other significant SNPs (rs314787954, rs13623466, rs13910430, and rs737507850) all located on chromosome 1 were strongly (p ≤ 7.6E-5) associated with chicken antibody response to ND. The closest genes to these four SNPs were cell division cycle 16 (CDC16), zinc finger, BED-type containing 1 (ZBED1), myxovirus (influenza virus) resistance 1 (MX1), and growth factor receptor bound protein 2 (GRB2) related adaptor protein 2 (GRAP2). Besides, other SNPs and genes suggestively (p ≤ 1.5E-5) associated with BW and antibody response to ND were reported. This work offers a useful entry point for the discovery of causative genes accountable for essential QTLs regulating BW and antibody response to ND traits. Results provide auspicious genes and SNP-based markers that can be used in the improvement of growth performance and ND resistance in IC populations based on gene-based and/or marker-assisted breeding selection.
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Affiliation(s)
- Richard Habimana
- College of Agriculture, Animal Science and Veterinary Medicine, University of Rwanda, Kigali, Rwanda.,Animal Breeding and Genomics Group, Department of Animal Science, Egerton University, Egerton, Kenya
| | - Kiplangat Ngeno
- Animal Breeding and Genomics Group, Department of Animal Science, Egerton University, Egerton, Kenya
| | - Tobias Otieno Okeno
- Animal Breeding and Genomics Group, Department of Animal Science, Egerton University, Egerton, Kenya
| | | | - Christian Keambou Tiambo
- Centre for Tropical Livestock Genetics and Health, International Livestock Research Institute, Nairobi, Kenya
| | - Nasser Kouadio Yao
- Biosciences Eastern and Central Africa - International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
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108
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Bhat JA, Yu D, Bohra A, Ganie SA, Varshney RK. Features and applications of haplotypes in crop breeding. Commun Biol 2021; 4:1266. [PMID: 34737387 PMCID: PMC8568931 DOI: 10.1038/s42003-021-02782-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/09/2021] [Indexed: 12/17/2022] Open
Abstract
Climate change with altered pest-disease dynamics and rising abiotic stresses threatens resource-constrained agricultural production systems worldwide. Genomics-assisted breeding (GAB) approaches have greatly contributed to enhancing crop breeding efficiency and delivering better varieties. Fast-growing capacity and affordability of DNA sequencing has motivated large-scale germplasm sequencing projects, thus opening exciting avenues for mining haplotypes for breeding applications. This review article highlights ways to mine haplotypes and apply them for complex trait dissection and in GAB approaches including haplotype-GWAS, haplotype-based breeding, haplotype-assisted genomic selection. Improvement strategies that efficiently deploy superior haplotypes to hasten breeding progress will be key to safeguarding global food security.
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Affiliation(s)
- Javaid Akhter Bhat
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Deyue Yu
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Abhishek Bohra
- Crop Improvement Division, ICAR- Indian Institute of Pulses Research (ICAR- IIPR), Kanpur, India
| | - Showkat Ahmad Ganie
- Department of Biotechnology, Visva-Bharati, Santiniketan, 731235, WB, India.
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.
- State Agricultural Biotechnology Centre, Centre for Crop & Food Research Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia.
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109
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Yang Z, Sun F, Liao H, Zhang Z, Dou Z, Xing Q, Hu J, Huang X, Bao Z. Genome-wide association study reveals genetic variations associated with ocean acidification resilience in Yesso scallop Patinopecten yessoensis. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 240:105963. [PMID: 34547702 DOI: 10.1016/j.aquatox.2021.105963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 08/22/2021] [Accepted: 09/04/2021] [Indexed: 06/13/2023]
Abstract
Ocean acidification (OA), which refers to a gradual decrease in seawater pH due to the absorption of atmospheric carbon dioxide, profoundly affects the growth, development and survival of bivalves. Relatively limited studies have assessed the resilience of bivalve to OA. In the present study, Patinopecten yessoensis, an economically and ecologically significant species, were exposed to low pH (pH = 7.5) for 4 weeks. Forty-seven scallops that died in the first week were considered pH-sensitive population, and 20 that were alive at the end of the experiment were considered pH-tolerant population. A genome-wide association study was conducted to identify the genomic loci associated the resilience of P. yessoensis to OA. Twenty-one single nucleotide polymorphisms were significantly associated with resilience, which were distributed in 11 linkage groups. Within the linkage disequilibrium block region (± 300 kb) surrounding the 21 SNPs, 193 candidate genes were successfully identified. Particularly, five associated SNPs were directly located on five genes, including SP24, CFDH, 5HTR3, HSDL1 and ZFP346. The GO enrichment and KEGG pathway analyses showed that the molecular response of P. yessoensis to OA mainly involved neural signal transmission, energy metabolism and redox reaction. Candidate genes were expressed during larval development and in adult tissues. Furthermore, the expression of 30 candidate genes changed significantly under low pH stress in the mantle. Our results reveal certain SNPs and candidate genes that could elucidate the different responses of P. yessoensis to OA. The genetic variations indicated molecular resilience in P. yessoensis populations, which may enable adaptation to future acidification stress.
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Affiliation(s)
- Zujing Yang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Fanhua Sun
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Huan Liao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China; College of Animal Biotechnology, Jiangxi Agricultural University, Nanchang, China
| | - Zhengrui Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zheng Dou
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Qiang Xing
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Xiaoting Huang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
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110
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Bellucci E, Mario Aguilar O, Alseekh S, Bett K, Brezeanu C, Cook D, De la Rosa L, Delledonne M, Dostatny DF, Ferreira JJ, Geffroy V, Ghitarrini S, Kroc M, Kumar Agrawal S, Logozzo G, Marino M, Mary‐Huard T, McClean P, Meglič V, Messer T, Muel F, Nanni L, Neumann K, Servalli F, Străjeru S, Varshney RK, Vasconcelos MW, Zaccardelli M, Zavarzin A, Bitocchi E, Frontoni E, Fernie AR, Gioia T, Graner A, Guasch L, Prochnow L, Oppermann M, Susek K, Tenaillon M, Papa R. The INCREASE project: Intelligent Collections of food-legume genetic resources for European agrofood systems. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:646-660. [PMID: 34427014 PMCID: PMC9293105 DOI: 10.1111/tpj.15472] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/11/2021] [Accepted: 08/17/2021] [Indexed: 05/14/2023]
Abstract
Food legumes are crucial for all agriculture-related societal challenges, including climate change mitigation, agrobiodiversity conservation, sustainable agriculture, food security and human health. The transition to plant-based diets, largely based on food legumes, could present major opportunities for adaptation and mitigation, generating significant co-benefits for human health. The characterization, maintenance and exploitation of food-legume genetic resources, to date largely unexploited, form the core development of both sustainable agriculture and a healthy food system. INCREASE will implement, on chickpea (Cicer arietinum), common bean (Phaseolus vulgaris), lentil (Lens culinaris) and lupin (Lupinus albus and L. mutabilis), a new approach to conserve, manage and characterize genetic resources. Intelligent Collections, consisting of nested core collections composed of single-seed descent-purified accessions (i.e., inbred lines), will be developed, exploiting germplasm available both from genebanks and on-farm and subjected to different levels of genotypic and phenotypic characterization. Phenotyping and gene discovery activities will meet, via a participatory approach, the needs of various actors, including breeders, scientists, farmers and agri-food and non-food industries, exploiting also the power of massive metabolomics and transcriptomics and of artificial intelligence and smart tools. Moreover, INCREASE will test, with a citizen science experiment, an innovative system of conservation and use of genetic resources based on a decentralized approach for data management and dynamic conservation. By promoting the use of food legumes, improving their quality, adaptation and yield and boosting the competitiveness of the agriculture and food sector, the INCREASE strategy will have a major impact on economy and society and represents a case study of integrative and participatory approaches towards conservation and exploitation of crop genetic resources.
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Affiliation(s)
- Elisa Bellucci
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marchevia Brecce BiancheAncona60131Italy
| | - Orlando Mario Aguilar
- Instituto de Biotecnología y Biología MolecularUNLP‐CONICETCCT La PlataLa PlataArgentina
| | - Saleh Alseekh
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm MüePotsdam‐Golm14476Germany
- Centre of Plant Systems Biology and BiotechnologyPlovdiv4000Bulgaria
| | - Kirstin Bett
- Department of Plant SciencesUniversity of Saskatchewan51 Campus DriveSaskatoonSKS7N 5A8Canada
| | - Creola Brezeanu
- Staţiunea de Cercetare Dezvoltare Pentru LegumiculturăBacău600388Romania
| | - Douglas Cook
- Department of Plant PathologyUniversity of California DavisDavisCA95616‐8680USA
| | - Lucía De la Rosa
- Spanish Plant Genetic Resources National Center (INIA, CRF)National Institute for Agricultural and Food Research and TechnologyAlcalá de HenaresMadrid28800Spain
| | - Massimo Delledonne
- Department of BiotechnologyUniversity of VeronaStrada Le Grazie 15Verona37134Italy
| | - Denise F. Dostatny
- National Centre for Plant Genetic Resources, Plant Breeding and Acclimatization Institute‐NRIRadzikówBłonie05‐870Poland
| | - Juan J. Ferreira
- Regional Service for Agrofood Research and Development (SERIDA)Ctra AS‐267, PK 19VillaviciosaAsturias33300Spain
| | - Valérie Geffroy
- CNRSINRAEInstitute of Plant Sciences Paris‐Saclay (IPS2)Univ EvryUniversité Paris‐SaclayOrsay91405France
- CNRSINRAEInstitute of Plant Sciences Paris Saclay (IPS2)Université de ParisOrsay91405France
| | | | - Magdalena Kroc
- Legume Genomics TeamInstitute of Plant GeneticsPolish Academy of SciencesStrzeszynska 34Poznan60‐479Poland
| | - Shiv Kumar Agrawal
- Genetic Resources SectionInternational Center for Agricultural Research in the Dry AreasICARDAAgdal RabatMorocco
| | - Giuseppina Logozzo
- School of Agricultural, Forestry, Food and Environmental SciencesUniversity of BasilicataPotenza85100Italy
| | - Mario Marino
- International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA)Food and Agriculture Organization of the United Nations (FAO)Viale delle Terme di CaracallaRome00153Italy
| | - Tristan Mary‐Huard
- INRAECNRSAgroParisTechGénétique Quantitative et Evolution ‐ Le MoulonUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Phil McClean
- Department of Plant Sciences, Genomics and Bioinformatics ProgramNorth Dakota State UniversityFargoND58108USA
| | - Vladimir Meglič
- Crop Science DepartmentAgricultural Institute of SloveniaHacquetova ulica 17Ljubljana1000Slovenia
| | - Tamara Messer
- EURICE ‐ European Research and Project Office GmbHHeinrich‐Hertz‐Allee 1St. Ingbert66386Germany
| | - Frédéric Muel
- Terres InoviaInstitut Technique des oléagineux, des protéagineux eu du chanvren1 Av L. BrétignièresThiverval-Grignon78850France
| | - Laura Nanni
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marchevia Brecce BiancheAncona60131Italy
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeeland06466Germany
| | - Filippo Servalli
- Comunità del Mais Spinato di Gandino (MASP)Via XX Settembre, 5GandinoBergamo24024Italy
| | - Silvia Străjeru
- Suceava Genebank (BRGV)Bdul 1 Mai, nr. 17Suceava720224Romania
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB)International Crops Research Institute for the Semi- Arid Tropics (ICRISAT)PatancheruIndia
- State Agricultural Biotechnology CentreCentre for Crop and Food InnovationFood Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Marta W. Vasconcelos
- CBQF – Centro de Biotecnologia e Química Fina – Laboratório AssociadoEscola Superior de BiotecnologiaUniversidade Católica PortuguesaRua Diogo Botelho 1327Porto4169-005Portugal
| | - Massimo Zaccardelli
- Council for Agricultural Research and EconomicsResearch Centre for Vegetable and Ornamental CropsVia Cavalleggeri 25Pontecagnano‐FaianoSA84098Italy
| | - Aleksei Zavarzin
- Federal Research CenterThe N.I. Vavilov All‐Russian Institute of Plant Genetic ResourcesSt. Petersburg190031Russia
| | - Elena Bitocchi
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marchevia Brecce BiancheAncona60131Italy
| | - Emanuele Frontoni
- Department of Information EngineeringPolytechnic University of Marchevia Brecce BiancheAncona60131Italy
| | - Alisdair R. Fernie
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm MüePotsdam‐Golm14476Germany
- Centre of Plant Systems Biology and BiotechnologyPlovdiv4000Bulgaria
| | - Tania Gioia
- School of Agricultural, Forestry, Food and Environmental SciencesUniversity of BasilicataPotenza85100Italy
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeeland06466Germany
| | - Luis Guasch
- Spanish Plant Genetic Resources National Center (INIA, CRF)National Institute for Agricultural and Food Research and TechnologyAlcalá de HenaresMadrid28800Spain
| | - Lena Prochnow
- EURICE ‐ European Research and Project Office GmbHHeinrich‐Hertz‐Allee 1St. Ingbert66386Germany
| | - Markus Oppermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeeland06466Germany
| | - Karolina Susek
- Legume Genomics TeamInstitute of Plant GeneticsPolish Academy of SciencesStrzeszynska 34Poznan60‐479Poland
| | - Maud Tenaillon
- INRAECNRSAgroParisTechGénétique Quantitative et Evolution ‐ Le MoulonUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Roberto Papa
- Department of Agricultural, Food and Environmental SciencesPolytechnic University of Marchevia Brecce BiancheAncona60131Italy
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Siekmann D, Jansen G, Zaar A, Kilian A, Fromme FJ, Hackauf B. A Genome-Wide Association Study Pinpoints Quantitative Trait Genes for Plant Height, Heading Date, Grain Quality, and Yield in Rye ( Secale cereale L.). FRONTIERS IN PLANT SCIENCE 2021; 12:718081. [PMID: 34777409 PMCID: PMC8586073 DOI: 10.3389/fpls.2021.718081] [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: 05/31/2021] [Accepted: 09/22/2021] [Indexed: 06/03/2023]
Abstract
Rye is the only cross-pollinating Triticeae crop species. Knowledge of rye genes controlling complex-inherited traits is scarce, which, currently, largely disables the genomics assisted introgression of untapped genetic variation from self-incompatible germplasm collections in elite inbred lines for hybrid breeding. We report on the first genome-wide association study (GWAS) in rye based on the phenotypic evaluation of 526 experimental hybrids for plant height, heading date, grain quality, and yield in 2 years and up to 19 environments. We established a cross-validated NIRS calibration model as a fast, effective, and robust analytical method to determine grain quality parameters. We observed phenotypic plasticity in plant height and tiller number as a resource use strategy of rye under drought and identified increased grain arabinoxylan content as a striking phenotype in osmotically stressed rye. We used DArTseq™ as a genotyping-by-sequencing technology to reduce the complexity of the rye genome. We established a novel high-density genetic linkage map that describes the position of almost 19k markers and that allowed us to estimate a low genome-wide LD based on the assessed genetic diversity in elite germplasm. We analyzed the relationship between plant height, heading date, agronomic, as well as grain quality traits, and genotype based on 20k novel single-nucleotide polymorphism markers. In addition, we integrated the DArTseq™ markers in the recently established 'Lo7' reference genome assembly. We identified cross-validated SNPs in 'Lo7' protein-coding genes associated with all traits studied. These include associations of the WUSCHEL-related homeobox transcription factor DWT1 and grain yield, the DELLA protein gene SLR1 and heading date, the Ethylene overproducer 1-like protein gene ETOL1 and thousand-grain weight, protein and starch content, as well as the Lectin receptor kinase SIT2 and plant height. A Leucine-rich repeat receptor protein kinase and a Xyloglucan alpha-1,6-xylosyltransferase count among the cross-validated genes associated with water-extractable arabinoxylan content. This study demonstrates the power of GWAS, hybrid breeding, and the reference genome sequence in rye genetics research to dissect and identify the function of genes shaping genetic diversity in agronomic and grain quality traits of rye. The described links between genetic causes and phenotypic variation will accelerate genomics-enabled rye improvement.
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Affiliation(s)
- Dörthe Siekmann
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Sanitz, Germany
- HYBRO Saatzucht GmbH & Co. KG, Schenkenberg, Germany
| | - Gisela Jansen
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Sanitz, Germany
| | - Anne Zaar
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Sanitz, Germany
| | | | | | - Bernd Hackauf
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Sanitz, Germany
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Effectiveness of the Influence of Selected Essential Oils on the Growth of Parasitic Fusarium Isolated from Wheat Kernels from Central Europe. Molecules 2021; 26:molecules26216488. [PMID: 34770893 PMCID: PMC8588391 DOI: 10.3390/molecules26216488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 11/16/2022] Open
Abstract
The aim of the study was to determine the effectiveness of selected seven commercial essential oils (EsO) (grapefruit, lemongrass, tea tree (TTO), thyme, verbena, cajeput, and Litsea cubeba) on isolates of common Central European parasitic fungal species of Fusarium obtained from infected wheat kernels, and to evaluate the oils as potential natural fungicides. The study was conducted in 2 stages. At each stage, the fungicidal activity of EsO (with concentrations of 0.025; 0.05; 0.125; 0.25; 0.50; 1.0, and 2.0%) against Fusarium spp. was evaluated using the disc plate method and zones of growth inhibition were measured. At the first stage, the fungistatic activity of EsO was evaluated against four species of Fusarium from the Polish population (F. avenaceum FAPL, F. culmorum FCPL, F. graminearum FGPL and F. oxysporum FOPL). The correlation coefficient between the mycelial growth rate index (T) and the fungistatic activity (FA) was calculated. At the second stage, on the basis of the mycelium growth rate index, the effectiveness of the EsO in limiting the development of Fusarium isolates from the German population (F. culmorum FC1D, F. culmorum FC2D, F. graminearum FG1D, F. graminearum FG2D and F. poae FP0D) was assessed. The first and second stage results presented as a growth rate index were then used to indicate essential oils (as potential natural fungicides) effectively limiting the development of various common Central European parasitic species Fusarium spp. Finally, the sensitivity of four Fusarium isolates from the Polish population and five Fusarium isolates from the German population was compared. The data were compiled in STATISTICA 13.0 (StatSoft, Inc, CA, USA) at the significance level of 0.05. Fusarium isolates from the German population were generally more sensitive than those from the Polish population. The sensitivity of individual Fusarium species varied. Their vulnerability, regardless of the isolate origin, in order from the most to the least sensitive, is as follows: F. culmorum, F. graminearum, F. poae, F. avenaceum and F. oxysporum. The strongest fungicidal activity, similar to Funaben T, showed thyme oil (regardless of the concentration). Performance of citral oils (lemongrass and Litsea cubeba) was similar but at a concentration above 0.025%.
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113
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Waldmann P. A proximal LAVA method for genome-wide association and prediction of traits with mixed inheritance patterns. BMC Bioinformatics 2021; 22:523. [PMID: 34702175 PMCID: PMC8547073 DOI: 10.1186/s12859-021-04436-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genetic basis of phenotypic traits is highly variable and usually divided into mono-, oligo- and polygenic inheritance classes. Relatively few traits are known to be monogenic or oligogeneic. The majority of traits are considered to have a polygenic background. To what extent there are mixtures between these classes is unknown. The rapid advancement of genomic techniques makes it possible to directly map large amounts of genomic markers (GWAS) and predict unknown phenotypes (GWP). Most of the multi-marker methods for GWAS and GWP falls into one of two regularization frameworks. The first framework is based on [Formula: see text]-norm regularization (e.g. the LASSO) and is suitable for mono- and oligogenic traits, whereas the second framework regularize with the [Formula: see text]-norm (e.g. ridge regression; RR) and thereby is favourable for polygenic traits. A general framework for mixed inheritance is lacking. RESULTS We have developed a proximal operator algorithm based on the recent LAVA regularization method that jointly performs [Formula: see text]- and [Formula: see text]-norm regularization. The algorithm is built on the alternating direction method of multipliers and proximal translation mapping (LAVA ADMM). When evaluated on the simulated QTLMAS2010 data, it is shown that the LAVA ADMM together with Bayesian optimization of the regularization parameters provides an efficient approach with lower test prediction mean-squared-error (65.89) than the LASSO (66.11), Ridge regression (83.41) and Elastic net (66.11). For the real pig data the test MSE of the LAVA ADMM is 0.850 compared to the LASSO, RR and EN with 0.875, 0.853 and 0.853, respectively. CONCLUSIONS This study presents the LAVA ADMM that is capable of joint modelling of monogenic major genetic effects and polygenic minor genetic effects which can be used for both genome-wide assoiciation and prediction purposes. The statistical evaluations based on both simulated and real pig data set shows that the LAVA ADMM has better prediction properies than the LASSO, RR and EN. Julia code for the LAVA ADMM is available at: https://github.com/patwa67/LAVAADMM .
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Affiliation(s)
- Patrik Waldmann
- Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland.
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114
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Chevin LM, Leung C, Le Rouzic A, Uller T. Using phenotypic plasticity to understand the structure and evolution of the genotype-phenotype map. Genetica 2021; 150:209-221. [PMID: 34617196 DOI: 10.1007/s10709-021-00135-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/22/2021] [Indexed: 10/20/2022]
Abstract
Deciphering the genotype-phenotype map necessitates relating variation at the genetic level to variation at the phenotypic level. This endeavour is inherently limited by the availability of standing genetic variation, the rate of spontaneous mutation to novo genetic variants, and possible biases associated with induced mutagenesis. An interesting alternative is to instead rely on the environment as a source of variation. Many phenotypic traits change plastically in response to the environment, and these changes are generally underlain by changes in gene expression. Relating gene expression plasticity to the phenotypic plasticity of more integrated organismal traits thus provides useful information about which genes influence the development and expression of which traits, even in the absence of genetic variation. We here appraise the prospects and limits of such an environment-for-gene substitution for investigating the genotype-phenotype map. We review models of gene regulatory networks, and discuss the different ways in which they can incorporate the environment to mechanistically model phenotypic plasticity and its evolution. We suggest that substantial progress can be made in deciphering this genotype-environment-phenotype map, by connecting theory on gene regulatory network to empirical patterns of gene co-expression, and by more explicitly relating gene expression to the expression and development of phenotypes, both theoretically and empirically.
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Affiliation(s)
- Luis-Miguel Chevin
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France.
| | - Christelle Leung
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Arnaud Le Rouzic
- Laboratoire Évolution, Génomes, Comportement, Écologie, CNRS, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Tobias Uller
- Department of Biology, Lund University, Lund, Sweden
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115
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Gong H, Zhang XY, Zhu S, Jiang L, Zhu X, Fang Q, Wu R. Genetic Architecture of Multiphasic Growth Covariation as Revealed by a Nonlinear Mixed Mapping Framework. FRONTIERS IN PLANT SCIENCE 2021; 12:711219. [PMID: 34675947 PMCID: PMC8524055 DOI: 10.3389/fpls.2021.711219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/06/2021] [Indexed: 05/09/2023]
Abstract
Trait covariation during multiphasic growth is of crucial significance to optimal survival and reproduction during the entire life cycle. However, current analyses are mainly focused on the study of individual traits, but exploring how genes determine trait interdependence spanning multiphasic growth processes remains challenging. In this study, we constructed a nonlinear mixed mapping framework to explore the genetic mechanisms that regulate multiphasic growth changes between two complex traits and used this framework to study stem diameter and stem height in forest trees. The multiphasic nonlinear mixed mapping framework was implemented in system mapping, by which several key quantitative trait loci were found to interpret the process and pattern of stem wood growth by regulating the ecological interactions of stem apical and lateral growth. We quantified the timing and pattern of the vegetative phase transition between independently regulated, temporally coordinated processes. Furthermore, we visualized the genetic machinery of significant loci, including genetic effects, genetic contribution analysis, and the regulatory relationship between these markers in the network structure. We validated the utility of the new mapping framework experimentally via computer simulations. The results may improve our understanding of the evolution of development in changing environments.
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Affiliation(s)
- Huiying Gong
- College of Science, Beijing Forestry University, Beijing, China
| | - Xiao-Yu Zhang
- College of Science, Beijing Forestry University, Beijing, China
| | - Sheng Zhu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Libo Jiang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xuli Zhu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Qing Fang
- Faculty of Science, Yamagata University, Yamagata, Japan
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Departments of Public Health Sciences and Statistics, Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, United States
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116
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Zhang J, Zhang D, Fan Y, Li C, Xu P, Li W, Sun Q, Huang X, Zhang C, Wu L, Yang H, Wang S, Su X, Li X, Song Y, Wu ME, Lian X, Li Y. The identification of grain size genes by RapMap reveals directional selection during rice domestication. Nat Commun 2021; 12:5673. [PMID: 34584089 PMCID: PMC8478914 DOI: 10.1038/s41467-021-25961-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 09/10/2021] [Indexed: 11/09/2022] Open
Abstract
Cloning quantitative trait locus (QTL) is time consuming and laborious, which hinders the understanding of natural variation and genetic diversity. Here, we introduce RapMap, a method for rapid multi-QTL mapping by employing F2 gradient populations (F2GPs) constructed by minor-phenotypic-difference accessions. The co-segregation standard of the single-locus genetic models ensures simultaneous integration of a three-in-one framework in RapMap i.e. detecting a real QTL, confirming its effect, and obtaining its near-isogenic line-like line (NIL-LL). We demonstrate the feasibility of RapMap by cloning eight rice grain-size genes using 15 F2GPs in three years. These genes explain a total of 75% of grain shape variation. Allele frequency analysis of these genes using a large germplasm collection reveals directional selection of the slender and long grains in indica rice domestication. In addition, major grain-size genes have been strongly selected during rice domestication. We think application of RapMap in crops will accelerate gene discovery and genomic breeding.
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Affiliation(s)
- Juncheng Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Dejian Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yawei Fan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Cuicui Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Pengkun Xu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Wei Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Qi Sun
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xiaodong Huang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Chunyu Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Linyue Wu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Huaizhou Yang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Shiyu Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xiaomin Su
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xingxing Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yingying Song
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Meng-En Wu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xingming Lian
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Yibo Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
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Lo YH, Cheng HC, Hsiung CN, Yang SL, Wang HY, Peng CW, Chen CY, Lin KP, Kang ML, Chen CH, Chu HW, Lin CF, Lee MH, Liu Q, Satta Y, Lin CJ, Lin M, Chaw SM, Loo JH, Shen CY, Ko WY. Detecting Genetic Ancestry and Adaptation in the Taiwanese Han People. Mol Biol Evol 2021; 38:4149-4165. [PMID: 33170928 PMCID: PMC8476137 DOI: 10.1093/molbev/msaa276] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The Taiwanese people are composed of diverse indigenous populations and the Taiwanese Han. About 95% of the Taiwanese identify themselves as Taiwanese Han, but this may not be a homogeneous population because they migrated to the island from various regions of continental East Asia over a period of 400 years. Little is known about the underlying patterns of genetic ancestry, population admixture, and evolutionary adaptation in the Taiwanese Han people. Here, we analyzed the whole-genome single-nucleotide polymorphism genotyping data from 14,401 individuals of Taiwanese Han collected by the Taiwan Biobank and the whole-genome sequencing data for a subset of 772 people. We detected four major genetic ancestries with distinct geographic distributions (i.e., Northern, Southeastern, Japonic, and Island Southeast Asian ancestries) and signatures of population mixture contributing to the genomes of Taiwanese Han. We further scanned for signatures of positive natural selection that caused unusually long-range haplotypes and elevations of hitchhiked variants. As a result, we identified 16 candidate loci in which selection signals can be unambiguously localized at five single genes: CTNNA2, LRP1B, CSNK1G3, ASTN2, and NEO1. Statistical associations were examined in 16 metabolic-related traits to further elucidate the functional effects of each candidate gene. All five genes appear to have pleiotropic connections to various types of disease susceptibility and significant associations with at least one metabolic-related trait. Together, our results provide critical insights for understanding the evolutionary history and adaption of the Taiwanese Han population.
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Affiliation(s)
- Yun-Hua Lo
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Hsueh-Chien Cheng
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Chia-Ni Hsiung
- Institute of Biomedical Sciences, Academia Sinica, Taipei City, Taiwan
| | - Show-Ling Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei City, Taiwan
| | - Han-Yu Wang
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Chia-Wei Peng
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Chun-Yu Chen
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Kung-Ping Lin
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Mei-Ling Kang
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Chien-Hsiun Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei City, Taiwan
| | - Hou-Wei Chu
- Institute of Biomedical Sciences, Academia Sinica, Taipei City, Taiwan
| | | | - Mei-Hsuan Lee
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Quintin Liu
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Cheng-Jui Lin
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan
| | - Marie Lin
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei City, Taiwan
| | - Jun-Hun Loo
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan
| | - Chen-Yang Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei City, Taiwan
| | - Wen-Ya Ko
- Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
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118
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Giannini HM, Meyer NJ. Genetics of Acute Respiratory Distress Syndrome: Pathways to Precision. Crit Care Clin 2021; 37:817-834. [PMID: 34548135 DOI: 10.1016/j.ccc.2021.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Clinical risk factors alone fail to fully explain acute respiratory distress syndrome (ARDS) risk or ARDS death, suggesting that individual risk factors contribute. The goals of genomic ARDS studies include better mechanistic understanding, identifying dysregulated pathways that may be amenable to pharmacologic targeting, using genomic causal inference techniques to find measurable traits with meaning, and deconvoluting ARDS heterogeneity by proving reproducible subpopulations that may share a unique biology. This article discusses the latest advances in ARDS genomics, provides historical perspective, and highlights some of the ways that the coronavirus disease 2019 (COVID-19) pandemic is accelerating genomic ARDS research.
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Affiliation(s)
- Heather M Giannini
- University of Pennsylvania Perelman School of Medicine, 3400 Spruce Street, 5038 Gates Building, Philadelphia, PA 19104, USA
| | - Nuala J Meyer
- University of Pennsylvania Perelman School of Medicine, 3400 Spruce Street, 5038 Gates Building, Philadelphia, PA 19104, USA.
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Zhong Z, McDonald BA, Palma-Guerrero J. Tolerance to oxidative stress is associated with both oxidative stress response and inherent growth in a fungal wheat pathogen. Genetics 2021; 217:6029569. [PMID: 33724407 DOI: 10.1093/genetics/iyaa022] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 11/23/2020] [Indexed: 01/25/2023] Open
Abstract
Reactive oxygen species are toxic byproducts of aerobic respiration that are also important in mediating a diversity of cellular functions. Reactive oxygen species form an important component of plant defenses to inhibit microbial pathogens during pathogen-plant interactions. Tolerance to oxidative stress is likely to make a significant contribution to the viability and pathogenicity of plant pathogens, but the complex network of oxidative stress responses hinders identification of the genes contributing to this trait. Here, we employed a forward genetic approach to investigate the genetic architecture of oxidative stress tolerance in the fungal wheat pathogen Zymoseptoria tritici. We used quantitative trait locus (QTL) mapping of growth and melanization under axenic conditions in two cross-populations to identify genomic regions associated with tolerance to oxidative stress. We found that QTLs associated with growth under oxidative stress as well as inherent growth can affect oxidative stress tolerance, and we identified two uncharacterized genes in a major QTL associated with this trait. Our data suggest that melanization does not affect tolerance to oxidative stress, which differs from what was found for animal pathogens. This study provides a whole-genome perspective on the genetic basis of oxidative stress tolerance in a plant pathogen.
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Affiliation(s)
- Ziming Zhong
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, 8092 Zürich, Switzerland
| | - Bruce A McDonald
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, 8092 Zürich, Switzerland
| | - Javier Palma-Guerrero
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, 8092 Zürich, Switzerland.,Department of Biointeractions and Crop Protection, Rothamsted Research, AL5 2JQ Harpenden, UK
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Rida S, Maafi O, López-Malvar A, Revilla P, Riache M, Djemel A. Genetics of Germination and Seedling Traits under Drought Stress in a MAGIC Population of Maize. PLANTS (BASEL, SWITZERLAND) 2021; 10:1786. [PMID: 34579319 PMCID: PMC8468063 DOI: 10.3390/plants10091786] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 01/31/2023]
Abstract
Drought is one of the most detrimental abiotic stresses hampering seed germination, development, and productivity. Maize is more sensitive to drought than other cereals, especially at seedling stage. Our objective was to study genetic regulation of drought tolerance at germination and during seedling growth in maize. We evaluated 420 RIL with their parents from a multi-parent advanced generation inter-cross (MAGIC) population with PEG-induced drought at germination and seedling establishment. A genome-wide association study (GWAS) was carried out to identify genomic regions associated with drought tolerance. GWAS identified 28 and 16 SNPs significantly associated with germination and seedling traits under stress and well-watered conditions, respectively. Among the SNPs detected, two SNPs had significant associations with several traits with high positive correlations, suggesting a pleiotropic genetic control. Other SNPs were located in regions that harbored major QTLs in previous studies, and co-located with QTLs for cold tolerance previously published for this MAGIC population. The genomic regions comprised several candidate genes related to stresses and plant development. These included numerous drought-responsive genes and transcription factors implicated in germination, seedling traits, and drought tolerance. The current analyses provide information and tools for subsequent studies and breeding programs for improving drought tolerance.
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Affiliation(s)
- Soumeya Rida
- Higher National Agronomic School (ENSA), L-RGB, Hassan Badi, El Harrach, Algiers 16004, Algeria; (S.R.); (O.M.); (M.R.); (A.D.)
| | - Oula Maafi
- Higher National Agronomic School (ENSA), L-RGB, Hassan Badi, El Harrach, Algiers 16004, Algeria; (S.R.); (O.M.); (M.R.); (A.D.)
| | - Ana López-Malvar
- Facultad de Biología, Departamento de Biología Vegetal y Ciencias del Suelo, Agrobiología Ambiental, Calidad de Suelos y Plantas, Universidad de Vigo, As Lagoas Marcosende, 36310 Vigo, Spain
| | - Pedro Revilla
- Misión Biológica de Galicia (CSIC), Apartado 28, E-36080 Pontevedra, Spain;
| | - Meriem Riache
- Higher National Agronomic School (ENSA), L-RGB, Hassan Badi, El Harrach, Algiers 16004, Algeria; (S.R.); (O.M.); (M.R.); (A.D.)
| | - Abderahmane Djemel
- Higher National Agronomic School (ENSA), L-RGB, Hassan Badi, El Harrach, Algiers 16004, Algeria; (S.R.); (O.M.); (M.R.); (A.D.)
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121
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Feldmann MJ, Piepho HP, Bridges WC, Knapp SJ. Average semivariance yields accurate estimates of the fraction of marker-associated genetic variance and heritability in complex trait analyses. PLoS Genet 2021; 17:e1009762. [PMID: 34437540 PMCID: PMC8425577 DOI: 10.1371/journal.pgen.1009762] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 09/08/2021] [Accepted: 08/09/2021] [Indexed: 12/15/2022] Open
Abstract
The development of genome-informed methods for identifying quantitative trait loci (QTL) and studying the genetic basis of quantitative variation in natural and experimental populations has been driven by advances in high-throughput genotyping. For many complex traits, the underlying genetic variation is caused by the segregation of one or more ‘large-effect’ loci, in addition to an unknown number of loci with effects below the threshold of statistical detection. The large-effect loci segregating in populations are often necessary but not sufficient for predicting quantitative phenotypes. They are, nevertheless, important enough to warrant deeper study and direct modelling in genomic prediction problems. We explored the accuracy of statistical methods for estimating the fraction of marker-associated genetic variance (p) and heritability ( HM2) for large-effect loci underlying complex phenotypes. We found that commonly used statistical methods overestimate p and HM2. The source of the upward bias was traced to inequalities between the expected values of variance components in the numerators and denominators of these parameters. Algebraic solutions for bias-correcting estimates of p and HM2 were found that only depend on the degrees of freedom and are constant for a given study design. We discovered that average semivariance methods, which have heretofore not been used in complex trait analyses, yielded unbiased estimates of p and HM2, in addition to best linear unbiased predictors of the additive and dominance effects of the underlying loci. The cryptic bias problem described here is unrelated to selection bias, although both cause the overestimation of p and HM2. The solutions we described are predicted to more accurately describe the contributions of large-effect loci to the genetic variation underlying complex traits of medical, biological, and agricultural importance. The contributions of individual genes to the phenotypic variation observed for genetically complex traits has been an ongoing and important challenge in biology, medicine, and agriculture. While many genes have statistically undetectable effects, those with large effects often warrant in-depth study and can be important predictors of complex phenotypes such as disease risk in humans or disease resistance in domesticated plants and animals. The genes identified through associations with genetic markers in complex trait analyses typically account for a fraction of the heritable variation, a genetic parameter we called ‘marker heritability’. We discovered that textbook statistical methods systematically overestimate marker heritability and thus overestimate the contributions of specific genes to the phenotypic variation observed for complex traits in natural and experimental populations. We describe the source of the upward bias, validate our findings through computer simulation, describe methods for bias-correcting estimates of marker heritability, and illustrate their application through empirical examples. The statistical methods we describe supply investigators with more accurate estimates of the contributions of specific genes or networks of interacting genes to the heritable variation observed in complex trait studies.
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Affiliation(s)
- Mitchell J. Feldmann
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Hans-Peter Piepho
- Biostatistics Unit, Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - William C. Bridges
- Department of Mathematical Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Steven J. Knapp
- Department of Plant Sciences, University of California, Davis, California, United States of America
- * E-mail:
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122
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DiFrisco J, Jaeger J. Genetic Causation in Complex Regulatory Systems: An Integrative Dynamic Perspective. Bioessays 2021; 42:e1900226. [PMID: 32449193 DOI: 10.1002/bies.201900226] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 03/01/2020] [Indexed: 12/27/2022]
Abstract
The logic of genetic discovery has changed little over time, but the focus of biology is shifting from simple genotype-phenotype relationships to complex metabolic, physiological, developmental, and behavioral traits. In light of this, the traditional reductionist view of individual genes as privileged difference-making causes of phenotypes is re-examined. The scope and nature of genetic effects in complex regulatory systems, in which dynamics are driven by regulatory feedback and hierarchical interactions across levels of organization are considered. This review argues that it is appropriate to treat genes as specific actual difference-makers for the molecular regulation of gene expression. However, they are often neither stable, proportional, nor specific as causes of the overall dynamic behavior of regulatory networks. Dynamical models, properly formulated and validated, provide the tools to probe cause-and-effect relationships in complex biological systems, allowing to go beyond the limitations of genetic reductionism to gain an integrative understanding of the causal processes underlying complex phenotypes.
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Affiliation(s)
| | - Johannes Jaeger
- Complexity Science Hub (CSH) Vienna, Josefstädter Straße 39, Vienna, 1080, Austria.,Department of Molecular Evolution & Development, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
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123
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Carley LN, Mojica JP, Wang B, Chen CY, Lin YP, Prasad KVSK, Chan E, Hsu CW, Keith R, Nuñez CL, Olson-Manning CF, Rushworth CA, Wagner MR, Wang J, Yeh PM, Reichelt M, Ghattas K, Gershenzon J, Lee CR, Mitchell-Olds T. Ecological factors influence balancing selection on leaf chemical profiles of a wildflower. Nat Ecol Evol 2021; 5:1135-1144. [PMID: 34140651 PMCID: PMC8325631 DOI: 10.1038/s41559-021-01486-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/07/2021] [Indexed: 02/05/2023]
Abstract
Balancing selection is frequently invoked as a mechanism that maintains variation within and across populations. However, there are few examples of balancing selection operating on loci underpinning complex traits, which frequently display high levels of variation. We investigated mechanisms that may maintain variation in a focal polymorphism-leaf chemical profiles of a perennial wildflower (Boechera stricta, Brassicaceae)-explicitly interrogating multiple ecological and genetic processes including spatial variation in selection, antagonistic pleiotropy and frequency-dependent selection. A suite of common garden and greenhouse experiments showed that the alleles underlying variation in chemical profile have contrasting fitness effects across environments, implicating two ecological drivers of selection on chemical profile: herbivory and drought. Phenotype-environment associations and molecular genetic analyses revealed additional evidence of past selection by these drivers. Together, these data are consistent with balancing selection on chemical profile, probably caused by pleiotropic effects of secondary chemical biosynthesis genes on herbivore defence and drought response.
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Affiliation(s)
- Lauren N Carley
- Duke University Program in Ecology, Durham, NC, USA
- Biology Department, Duke University, Durham, NC, USA
- Rocky Mountain Biological Laboratory, Gothic, CO, USA
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St Paul, MN, USA
| | - Julius P Mojica
- Biology Department, Duke University, Durham, NC, USA
- Pairwise Plants, Durham, NC, USA
| | - Baosheng Wang
- Biology Department, Duke University, Durham, NC, USA
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Chia-Yu Chen
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
| | - Ya-Ping Lin
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
- World Vegetable Center Headquarters, Tainan, Taiwan
| | - Kasavajhala V S K Prasad
- Department of Biology and Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, USA
| | - Emily Chan
- Biology Department, Duke University, Durham, NC, USA
| | - Che-Wei Hsu
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
- Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
- The Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Rose Keith
- Biology Department, Duke University, Durham, NC, USA
- Biology Department, DePauw University, Greencastle, IN, USA
| | - Chase L Nuñez
- Duke University Program in Ecology, Durham, NC, USA
- Department for the Ecology of Animal Societies, Max Planck Institute of Animal Behavior, Baden-Württemberg, Germany
| | - Carrie F Olson-Manning
- Biology Department, Duke University, Durham, NC, USA
- Augustana University, Sioux Falls, SD, USA
| | - Catherine A Rushworth
- Biology Department, Duke University, Durham, NC, USA
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St Paul, MN, USA
- Evolution and Ecology Department, University of California Davis, Davis, CA, USA
- University and Jepson Herbaria, University of California Berkeley, Berkeley, CA, USA
| | - Maggie R Wagner
- Biology Department, Duke University, Durham, NC, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
- Kansas Biological Survey, Lawrence, KS, USA
| | - Jing Wang
- Biology Department, Duke University, Durham, NC, USA
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Pei-Min Yeh
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan
| | - Michael Reichelt
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | | | - Jonathan Gershenzon
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Cheng-Ruei Lee
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, Taiwan.
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan.
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan.
| | - Thomas Mitchell-Olds
- Biology Department, Duke University, Durham, NC, USA.
- Rocky Mountain Biological Laboratory, Gothic, CO, USA.
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124
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Miculan M, Nelissen H, Ben Hassen M, Marroni F, Inzé D, Pè ME, Dell’Acqua M. A forward genetics approach integrating genome-wide association study and expression quantitative trait locus mapping to dissect leaf development in maize (Zea mays). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1056-1071. [PMID: 34087008 PMCID: PMC8519057 DOI: 10.1111/tpj.15364] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 05/31/2021] [Indexed: 05/13/2023]
Abstract
The characterization of the genetic basis of maize (Zea mays) leaf development may support breeding efforts to obtain plants with higher vigor and productivity. In this study, a mapping panel of 197 biparental and multiparental maize recombinant inbred lines (RILs) was analyzed for multiple leaf traits at the seedling stage. RNA sequencing was used to estimate the transcription levels of 29 573 gene models in RILs and to derive 373 769 single nucleotide polymorphisms (SNPs), and a forward genetics approach combining these data was used to pinpoint candidate genes involved in leaf development. First, leaf traits were correlated with gene expression levels to identify transcript-trait correlations. Then, leaf traits were associated with SNPs in a genome-wide association (GWA) study. An expression quantitative trait locus mapping approach was followed to associate SNPs with gene expression levels, prioritizing candidate genes identified based on transcript-trait correlations and GWAs. Finally, a network analysis was conducted to cluster all transcripts in 38 co-expression modules. By integrating forward genetics approaches, we identified 25 candidate genes highly enriched for specific functional categories, providing evidence supporting the role of vacuolar proton pumps, cell wall effectors, and vesicular traffic controllers in leaf growth. These results tackle the complexity of leaf trait determination and may support precision breeding in maize.
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Affiliation(s)
- Mara Miculan
- Institute of Life SciencesScuola Superiore Sant’AnnaPisa56127Italy
| | - Hilde Nelissen
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhent9052Belgium
- Center for Plant Systems Biology, VIBGhent9052Belgium
| | - Manel Ben Hassen
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhent9052Belgium
- Center for Plant Systems Biology, VIBGhent9052Belgium
| | - Fabio Marroni
- IGA Technology ServicesUdine33100Italy
- Department of Agricultural, FoodAT, Environmental and Animal Sciences (DI4A)University of UdineUdine33100Italy
| | - Dirk Inzé
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhent9052Belgium
- Center for Plant Systems Biology, VIBGhent9052Belgium
| | - Mario Enrico Pè
- Institute of Life SciencesScuola Superiore Sant’AnnaPisa56127Italy
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125
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Buchberger E, Bilen A, Ayaz S, Salamanca D, Matas de las Heras C, Niksic A, Almudi I, Torres-Oliva M, Casares F, Posnien N. Variation in Pleiotropic Hub Gene Expression Is Associated with Interspecific Differences in Head Shape and Eye Size in Drosophila. Mol Biol Evol 2021; 38:1924-1942. [PMID: 33386848 PMCID: PMC8097299 DOI: 10.1093/molbev/msaa335] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Revealing the mechanisms underlying the breathtaking morphological diversity observed in nature is a major challenge in Biology. It has been established that recurrent mutations in hotspot genes cause the repeated evolution of morphological traits, such as body pigmentation or the gain and loss of structures. To date, however, it remains elusive whether hotspot genes contribute to natural variation in the size and shape of organs. As natural variation in head morphology is pervasive in Drosophila, we studied the molecular and developmental basis of differences in compound eye size and head shape in two closely related Drosophila species. We show differences in the progression of retinal differentiation between species and we applied comparative transcriptomics and chromatin accessibility data to identify the GATA transcription factor Pannier (Pnr) as central factor associated with these differences. Although the genetic manipulation of Pnr affected multiple aspects of dorsal head development, the effect of natural variation is restricted to a subset of the phenotypic space. We present data suggesting that this developmental constraint is caused by the coevolution of expression of pnr and its cofactor u-shaped (ush). We propose that natural variation in expression or function of highly connected developmental regulators with pleiotropic functions is a major driver for morphological evolution and we discuss implications on gene regulatory network evolution. In comparison to previous findings, our data strongly suggest that evolutionary hotspots are not the only contributors to the repeated evolution of eye size and head shape in Drosophila.
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Affiliation(s)
- Elisa Buchberger
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
| | - Anıl Bilen
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
| | - Sanem Ayaz
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
| | - David Salamanca
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
- Present address: Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | | | - Armin Niksic
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
| | - Isabel Almudi
- CABD (CSIC/UPO/JA), DMC2 Unit, Pablo de Olavide University Campus, Seville, Spain
| | - Montserrat Torres-Oliva
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
- Present address: Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Fernando Casares
- CABD (CSIC/UPO/JA), DMC2 Unit, Pablo de Olavide University Campus, Seville, Spain
| | - Nico Posnien
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
- Corresponding author: E-mail:
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126
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Quantitative trait loci for growth-related traits in Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing. Mol Genet Genomics 2021; 296:1147-1159. [PMID: 34251529 DOI: 10.1007/s00438-021-01806-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/16/2021] [Indexed: 10/20/2022]
Abstract
This study aimed to identify quantitative trait loci (QTLs) for growth-related traits by constructing a genetic linkage map based on single nucleotide polymorphism (SNP) markers in Japanese quail. A QTL mapping population of 277 F2 birds was obtained from an intercross between a male of a large-sized strain and three females of a normal-sized strain. Body weight (BW) was measured weekly from hatching to 16 weeks of age. Non-linear regression growth models of Weibull, Logistic, Gompertz, Richards, and Brody were analyzed, and growth curve parameters of Richards was selected as the best model to describe the quail growth curve of the F2 birds. Restriction-site associated DNA sequencing developed 125 SNP markers that were informative between their parental strains. The SNP markers were distributed on 16 linkage groups that spanned 795.9 centiMorgan (cM) with an average marker interval of 7.3 cM. QTL analysis of phenotypic traits revealed four main-effect QTLs. Detected QTLs were located on chromosomes 1 and 3 and were associated with BW from 4 to 16 weeks of age and asymptotic weight of Richards model at genome-wide significant at 1% or 5% level. No QTL was detected for BW from 0 to 3 weeks of age. This is the first report identified QTLs for asymptotic weight of the Richards parameter in Japanese quail. These results highlight that the combination of QTL studies and the RAD-seq method will aid future breeding programs identify genes underlying the QTL and the application of marker-assisted selection in the poultry industry, particularly the Japanese quail.
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127
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scLink: Inferring Sparse Gene Co-expression Networks from Single-cell Expression Data. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:475-492. [PMID: 34252628 PMCID: PMC8896229 DOI: 10.1016/j.gpb.2020.11.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/23/2020] [Accepted: 12/26/2020] [Indexed: 11/23/2022]
Abstract
A system-level understanding of the regulation and coordination mechanisms of gene expression is essential for studying the complexity of biological processes in health and disease. With the rapid development of single-cell RNA sequencing technologies, it is now possible to investigate gene interactions in a cell type-specific manner. Here we propose the scLink method, which uses statistical network modeling to understand the co-expression relationships among genes and construct sparse gene co-expression networks from single-cell gene expression data. We use both simulation and real data studies to demonstrate the advantages of scLink and its ability to improve single-cell gene network analysis. The scLink R package is available at https://github.com/Vivianstats/scLink.
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128
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Liu H, Song H, Jiang Y, Jiang Y, Zhang F, Liu Y, Shi Y, Ding X, Wang C. A Single-Step Genome Wide Association Study on Body Size Traits Using Imputation-Based Whole-Genome Sequence Data in Yorkshire Pigs. Front Genet 2021; 12:629049. [PMID: 34276758 PMCID: PMC8283822 DOI: 10.3389/fgene.2021.629049] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
The body shape of a pig is the most direct production index, which can fully reflect the pig’s growth status and is closely related to important economic traits. In this study, a genome-wide association study on seven body size traits, the body length (BL), height (BH), chest circumference (CC), abdominal circumference (AC), cannon bone circumference (CBC), rump width (RW), and chest width (CW), were conducted in Yorkshire pigs. Illumina Porcine 80K SNP chips were used to genotype 589 of 5,572 Yorkshire pigs with body size records, and then the chip data was imputed to sequencing data. After quality control of imputed sequencing data, 784,267 SNPs were obtained, and the averaged linkage disequilibrium (r2) was 0.191. We used the single-trait model and the two-trait model to conduct single-step genome wide association study (ssGWAS) on seven body size traits; a total of 198 significant SNPS were finally identified according to the P-value and the contribution to the genetic variance of individual SNP. 11 candidate genes (CDH13, SIL1, CDC14A, TMRPSS15, TRAPPC9, CTNND2, KDM6B, CHD3, MUC13, MAPK4, and HMGA1) were found to be associated with body size traits in pigs; KDM6B and CHD3 jointly affect AC and CC, and MUC13 jointly affect RW and CW. These genes are involved in the regulation of bone growth and development as well as the absorption of nutrients and are associated with obesity. HMGA1 is proposed as a strong candidate gene for body size traits because of its important function and high consistency with other studies regarding the regulation of body size traits. Our results could provide valuable information for pig breeding based on molecular breeding.
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Affiliation(s)
- Huatao Liu
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hailiang Song
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yifan Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yao Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Fengxia Zhang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yibing Liu
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yong Shi
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiangdong Ding
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chuduan Wang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
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129
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Götz FM, Gosling SD, Rentfrow PJ. Small Effects: The Indispensable Foundation for a Cumulative Psychological Science. PERSPECTIVES ON PSYCHOLOGICAL SCIENCE 2021; 17:205-215. [PMID: 34213378 DOI: 10.1177/1745691620984483] [Citation(s) in RCA: 144] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We draw on genetics research to argue that complex psychological phenomena are most likely determined by a multitude of causes and that any individual cause is likely to have only a small effect. Building on this, we highlight the dangers of a publication culture that continues to demand large effects. First, it rewards inflated effects that are unlikely to be real and encourages practices likely to yield such effects. Second, it overlooks the small effects that are most likely to be real, hindering attempts to identify and understand the actual determinants of complex psychological phenomena. We then explain the theoretical and practical relevance of small effects, which can have substantial consequences, especially when considered at scale and over time. Finally, we suggest ways in which scholars can harness these insights to advance research and practices in psychology (i.e., leveraging the power of big data, machine learning, and crowdsourcing science; promoting rigorous preregistration, including prespecifying the smallest effect size of interest; contextualizing effects; changing cultural norms to reward accurate and meaningful effects rather than exaggerated and unreliable effects). Only once small effects are accepted as the norm, rather than the exception, can a reliable and reproducible cumulative psychological science be built.
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Affiliation(s)
- Friedrich M Götz
- Department of Psychology, University of Cambridge.,Department of Psychology, University of British Columbia
| | - Samuel D Gosling
- Department of Psychology, University of Texas at Austin.,Melbourne School of Psychological Sciences, University of Melbourne
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130
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Woods P, Campbell BJ, Nicodemus TJ, Cahoon EB, Mullen JL, McKay JK. Quantitative Trait Loci Controlling Agronomic and Biochemical Traits in Cannabis sativa. Genetics 2021; 219:6310019. [PMID: 34173826 PMCID: PMC9335937 DOI: 10.1093/genetics/iyab099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/15/2021] [Indexed: 11/23/2022] Open
Abstract
Understanding the genetic basis of complex traits is a fundamental goal of evolutionary genetics. Yet, the genetics controlling complex traits in many important species such as hemp (Cannabis sativa) remain poorly investigated. Because hemp’s change in legal status with the 2014 and 2018 U.S. Federal Farm Bills, interest in the genetics controlling its numerous agriculturally important traits has steadily increased. To better understand the genetics of agriculturally important traits in hemp, we developed an F2 population by crossing two phenotypically distinct hemp cultivars (Carmagnola and USO31). Using whole-genome sequencing, we mapped quantitative trait loci (QTL) associated with variation in numerous agronomic and biochemical traits. A total of 69 loci associated with agronomic (34) and biochemical (35) trait variation were identified. We found that most QTL co-localized, suggesting that the phenotypic distinctions between Carmagnola and USO31 are largely controlled by a small number of loci. We identified TINY and olivetol synthase as candidate genes underlying co-localized QTL clusters for agronomic and biochemical traits, respectively. We functionally validated the olivetol synthase candidate by expressing the alleles in yeast. Gas chromatography-mass spectrometry assays of extracts from these yeast colonies suggest that the USO31 olivetol synthase is functionally less active and potentially explains why USO31 produces lower cannabinoids compared to Carmagnola. Overall, our results help modernize the genomic understanding of complex traits in hemp.
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Affiliation(s)
- Patrick Woods
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, 80523, United States of America.,Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, 80523, United States of America
| | - Brian J Campbell
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, 80523, United States of America
| | - Timothy J Nicodemus
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States of America
| | - Edgar B Cahoon
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States of America
| | - Jack L Mullen
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, 80523, United States of America
| | - John K McKay
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, 80523, United States of America
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131
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Liang Y, Liu HJ, Yan J, Tian F. Natural Variation in Crops: Realized Understanding, Continuing Promise. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:357-385. [PMID: 33481630 DOI: 10.1146/annurev-arplant-080720-090632] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Crops feed the world's population and shape human civilization. The improvement of crop productivity has been ongoing for almost 10,000 years and has evolved from an experience-based to a knowledge-driven practice over the past three decades. Natural alleles and their reshuffling are long-standing genetic changes that affect how crops respond to various environmental conditions and agricultural practices. Decoding the genetic basis of natural variation is central to understanding crop evolution and, in turn, improving crop breeding. Here, we review current advances in the approaches used to map the causal alleles of natural variation, provide refined insights into the genetics and evolution of natural variation, and outline how this knowledge promises to drive the development of sustainable agriculture under the dome of emerging technologies.
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Affiliation(s)
- Yameng Liang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; ,
| | - Hai-Jun Liu
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, 1030 Vienna, Austria;
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
| | - Feng Tian
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; ,
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132
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Guerra-García A, Gioia T, von Wettberg E, Logozzo G, Papa R, Bitocchi E, Bett KE. Intelligent Characterization of Lentil Genetic Resources: Evolutionary History, Genetic Diversity of Germplasm, and the Need for Well-Represented Collections. Curr Protoc 2021; 1:e134. [PMID: 34004055 DOI: 10.1002/cpz1.134] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The genetic and phenotypic characterization of crops allows us to elucidate their evolutionary and domestication history, the genetic basis of important traits, and the use of variation present in landraces and wild relatives to enhance resilience. In this context, we aim to provide an overview of the main genetic resources developed for lentil and their main outcomes, and to suggest protocols for continued work on this important crop. Lens culinaris is the third-most-important cool-season grain and its use is increasing as a quick-cooking, nutritious, plant-based source of protein. L. culinaris was domesticated in the Fertile Crescent, and six additional wild taxa (L. orientalis, L. tomentosus, L. odemensis, L. lamottei, L. ervoides, and L. nigricans) are recognized. Numerous genetic diversity studies have shown that wild relatives present high levels of genetic variation and provide a reservoir of alleles that can be used for breeding programs. Furthermore, the integration of genetics/genomics and breeding techniques has resulted in identification of quantitative trait loci and genes related to attributes of interest. Genetic maps, massive genotyping, marker-assisted selection, and genomic selection are some of the genetic resources generated and applied in lentil. In addition, despite its size (∼4 Gbp) and complexity, the L. culinaris genome has been assembled, allowing a deeper understanding of its architecture. Still, major knowledge gaps exist in lentil, and a deeper understanding and characterization of germplasm resources, including wild relatives, is critical to lentil breeding and improvement. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Recording of lentil seed descriptors Basic Protocol 2: Lentil seed imaging Basic Protocol 3: Lentil seed increase Basic Protocol 4: Recording of primary lentil seed INCREASE descriptors.
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Affiliation(s)
- Azalea Guerra-García
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Tania Gioia
- School of Agriculture, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - Eric von Wettberg
- Department of Plant and Soil Sciences and Gund Institute for the Environment, University of Vermont, Burlington, Vermont
| | - Giuseppina Logozzo
- School of Agriculture, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Elena Bitocchi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Kirstin E Bett
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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133
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Li X, Guo T, Wang J, Bekele WA, Sukumaran S, Vanous AE, McNellie JP, Tibbs-Cortes LE, Lopes MS, Lamkey KR, Westgate ME, McKay JK, Archontoulis SV, Reynolds MP, Tinker NA, Schnable PS, Yu J. An integrated framework reinstating the environmental dimension for GWAS and genomic selection in crops. MOLECULAR PLANT 2021; 14:874-887. [PMID: 33713844 DOI: 10.1016/j.molp.2021.03.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/03/2021] [Accepted: 03/09/2021] [Indexed: 05/08/2023]
Abstract
Identifying mechanisms and pathways involved in gene-environment interplay and phenotypic plasticity is a long-standing challenge. It is highly desirable to establish an integrated framework with an environmental dimension for complex trait dissection and prediction. A critical step is to identify an environmental index that is both biologically relevant and estimable for new environments. With extensive field-observed complex traits, environmental profiles, and genome-wide single nucleotide polymorphisms for three major crops (maize, wheat, and oat), we demonstrated that identifying such an environmental index (i.e., a combination of environmental parameter and growth window) enables genome-wide association studies and genomic selection of complex traits to be conducted with an explicit environmental dimension. Interestingly, genes identified for two reaction-norm parameters (i.e., intercept and slope) derived from flowering time values along the environmental index were less colocalized for a diverse maize panel than for wheat and oat breeding panels, agreeing with the different diversity levels and genetic constitutions of the panels. In addition, we showcased the usefulness of this framework for systematically forecasting the performance of diverse germplasm panels in new environments. This general framework and the companion CERIS-JGRA analytical package should facilitate biologically informed dissection of complex traits, enhanced performance prediction in breeding for future climates, and coordinated efforts to enrich our understanding of mechanisms underlying phenotypic variation.
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Affiliation(s)
- Xianran Li
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Tingting Guo
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Jinyu Wang
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Wubishet A Bekele
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Sivakumar Sukumaran
- International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
| | - Adam E Vanous
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - James P McNellie
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | | | - Marta S Lopes
- International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
| | - Kendall R Lamkey
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Mark E Westgate
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - John K McKay
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
| | | | - Matthew P Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
| | - Nicholas A Tinker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | | | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA.
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134
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Jovanovic VM, Sarfert M, Reyna-Blanco CS, Indrischek H, Valdivia DI, Shelest E, Nowick K. Positive Selection in Gene Regulatory Factors Suggests Adaptive Pleiotropic Changes During Human Evolution. Front Genet 2021; 12:662239. [PMID: 34079582 PMCID: PMC8166252 DOI: 10.3389/fgene.2021.662239] [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: 01/31/2021] [Accepted: 04/19/2021] [Indexed: 01/09/2023] Open
Abstract
Gene regulatory factors (GRFs), such as transcription factors, co-factors and histone-modifying enzymes, play many important roles in modifying gene expression in biological processes. They have also been proposed to underlie speciation and adaptation. To investigate potential contributions of GRFs to primate evolution, we analyzed GRF genes in 27 publicly available primate genomes. Genes coding for zinc finger (ZNF) proteins, especially ZNFs with a Krüppel-associated box (KRAB) domain were the most abundant TFs in all genomes. Gene numbers per TF family differed between all species. To detect signs of positive selection in GRF genes we investigated more than 3,000 human GRFs with their more than 70,000 orthologs in 26 non-human primates. We implemented two independent tests for positive selection, the branch-site-model of the PAML suite and aBSREL of the HyPhy suite, focusing on the human and great ape branch. Our workflow included rigorous procedures to reduce the number of false positives: excluding distantly similar orthologs, manual corrections of alignments, and considering only genes and sites detected by both tests for positive selection. Furthermore, we verified the candidate sites for selection by investigating their variation within human and non-human great ape population data. In order to approximately assign a date to positively selected sites in the human lineage, we analyzed archaic human genomes. Our work revealed with high confidence five GRFs that have been positively selected on the human lineage and one GRF that has been positively selected on the great ape lineage. These GRFs are scattered on different chromosomes and have been previously linked to diverse functions. For some of them a role in speciation and/or adaptation can be proposed based on the expression pattern or association with human diseases, but it seems that they all contributed independently to human evolution. Four of the positively selected GRFs are KRAB-ZNF proteins, that induce changes in target genes co-expression and/or through arms race with transposable elements. Since each positively selected GRF contains several sites with evidence for positive selection, we suggest that these GRFs participated pleiotropically to phenotypic adaptations in humans.
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Affiliation(s)
- Vladimir M Jovanovic
- Human Biology and Primate Evolution, Freie Universität Berlin, Berlin, Germany.,Bioinformatics Solution Center, Freie Universität Berlin, Berlin, Germany
| | - Melanie Sarfert
- Human Biology and Primate Evolution, Freie Universität Berlin, Berlin, Germany
| | - Carlos S Reyna-Blanco
- Department of Biology, University of Fribourg, Fribourg, Switzerland.,Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Henrike Indrischek
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| | - Dulce I Valdivia
- Evolutionary Genomics Laboratory and Genome Topology and Regulation Laboratory, Genetic Engineering Department, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-Irapuato), Irapuato, Mexico
| | - Ekaterina Shelest
- Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, United Kingdom
| | - Katja Nowick
- Human Biology and Primate Evolution, Freie Universität Berlin, Berlin, Germany
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135
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Laurent B, Moinard M, Spataro C, Chéreau S, Zehraoui E, Blanc R, Lasserre P, Ponts N, Foulongne-Oriol M. QTL mapping in Fusarium graminearum identified an allele of FgVe1 involved in reduced aggressiveness. Fungal Genet Biol 2021; 153:103566. [PMID: 33991664 DOI: 10.1016/j.fgb.2021.103566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 05/04/2021] [Accepted: 05/05/2021] [Indexed: 10/21/2022]
Abstract
Fusarium graminearum is one of the most frequent causal agents of the Fusarium Head Blight, a cereal disease spread throughout the world, reducing grain production and quality. F. graminearum isolates are genetically and phenotypically highly diverse. Notably, remarkable variations of aggressiveness between isolates have been observed, which could reflect an adaptive potential of this pathogen. In this study, we aimed to characterize the genetic basis of aggressiveness variation observed in an F1 population (n = 94), for which genome sequences of both parental strains are available. Aggressiveness was assessed by a panel of in planta and in vitro proxies during two phenotyping trials including, among others, disease severity and mycotoxin accumulation in wheat spike. One major and single QTL was mapped for all the traits measured, on chromosome I, that explained up to 90% of the variance for disease severity. The confidence interval at the QTL spanned 1.2 Mb and contained 428 genes on the reference genome. Of these, four candidates were selected based on the postulate that a non-synonymous mutation affecting protein function may be responsible for phenotypic differences. Finally, a new mutation was identified and functionally validated in the gene FgVe1, coding for a velvet protein known to be involved in pathogenicity and secondary metabolism production in several fungi.
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Affiliation(s)
| | | | | | | | - Enric Zehraoui
- INRAE, MycSA, F-33882 Villenave d'Ornon, France; Université de Bordeaux, INRAE, EGFV, F-33882 Villenave d'Ornon, France
| | - Richard Blanc
- INRAE, UCA, UMR 1095 GDEC, F-63100 Clermont-Ferrand, France
| | | | - Nadia Ponts
- INRAE, MycSA, F-33882 Villenave d'Ornon, France
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136
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Galán RJ, Bernal-Vasquez AM, Jebsen C, Piepho HP, Thorwarth P, Steffan P, Gordillo A, Miedaner T. Early prediction of biomass in hybrid rye based on hyperspectral data surpasses genomic predictability in less-related breeding material. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1409-1422. [PMID: 33630103 PMCID: PMC8081675 DOI: 10.1007/s00122-021-03779-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 01/19/2021] [Indexed: 05/15/2023]
Abstract
Hyperspectral data is a promising complement to genomic data to predict biomass under scenarios of low genetic relatedness. Sufficient environmental connectivity between data used for model training and validation is required. The demand for sustainable sources of biomass is increasing worldwide. The early prediction of biomass via indirect selection of dry matter yield (DMY) based on hyperspectral and/or genomic prediction is crucial to affordably untap the potential of winter rye (Secale cereale L.) as a dual-purpose crop. However, this estimation involves multiple genetic backgrounds and genetic relatedness is a crucial factor in genomic selection (GS). To assess the prospect of prediction using reflectance data as a suitable complement to GS for biomass breeding, the influence of trait heritability ([Formula: see text]) and genetic relatedness were compared. Models were based on genomic (GBLUP) and hyperspectral reflectance-derived (HBLUP) relationship matrices to predict DMY and other biomass-related traits such as dry matter content (DMC) and fresh matter yield (FMY). For this, 270 elite rye lines from nine interconnected bi-parental families were genotyped using a 10 k-SNP array and phenotyped as testcrosses at four locations in two years (eight environments). From 400 discrete narrow bands (410 nm-993 nm) collected by an uncrewed aerial vehicle (UAV) on two dates in each environment, 32 hyperspectral bands previously selected by Lasso were incorporated into a prediction model. HBLUP showed higher prediction abilities (0.41 - 0.61) than GBLUP (0.14 - 0.28) under a decreased genetic relationship, especially for mid-heritable traits (FMY and DMY), suggesting that HBLUP is much less affected by relatedness and [Formula: see text]. However, the predictive power of both models was largely affected by environmental variances. Prediction abilities for DMY were further enhanced (up to 20%) by integrating both matrices and plant height into a bivariate model. Thus, data derived from high-throughput phenotyping emerges as a suitable strategy to efficiently leverage selection gains in biomass rye breeding; however, sufficient environmental connectivity is needed.
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Affiliation(s)
- Rodrigo José Galán
- State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany
| | | | | | - Hans-Peter Piepho
- Biostatistics Unit, Institute of Crop Science, University of Hohenheim, 70593, Stuttgart, Germany
| | - Patrick Thorwarth
- State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany
- KWS SAAT SE, Grimsehlstraße 31, 37574, Einbeck, Germany
| | - Philipp Steffan
- KWS LOCHOW GMBH, Ferdinand-von-Lochow Straße 5, 29303, Bergen, Germany
| | - Andres Gordillo
- KWS LOCHOW GMBH, Ferdinand-von-Lochow Straße 5, 29303, Bergen, Germany
| | - Thomas Miedaner
- State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany.
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137
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Zhu M, Tong L, Xu M, Zhong T. Genetic dissection of maize disease resistance and its applications in molecular breeding. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:32. [PMID: 37309327 PMCID: PMC10236108 DOI: 10.1007/s11032-021-01219-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/25/2021] [Indexed: 06/14/2023]
Abstract
Disease resistance is essential for reliable maize production. In a long-term tug-of-war between maize and its pathogenic microbes, naturally occurring resistance genes gradually accumulate and play a key role in protecting maize from various destructive diseases. Recently, significant progress has been made in deciphering the genetic basis of disease resistance in maize. Enhancing disease resistance can now be explored at the molecular level, from marker-assisted selection to genomic selection, transgenesis technique, and genome editing. In view of the continuing accumulation of cloned resistance genes and in-depth understanding of their resistance mechanisms, coupled with rapid progress of biotechnology, it is expected that the large-scale commercial application of molecular breeding of resistant maize varieties will soon become a reality.
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Affiliation(s)
- Mang Zhu
- State Key Laboratory of Plant Physiology and Biochemistry/College of Agronomy and Biotechnology/National Maize Improvement Center/Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, 2 West Yuanmingyuan Road, Beijing, 100193 People’s Republic of China
| | - Lixiu Tong
- State Key Laboratory of Plant Physiology and Biochemistry/College of Agronomy and Biotechnology/National Maize Improvement Center/Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, 2 West Yuanmingyuan Road, Beijing, 100193 People’s Republic of China
| | - Mingliang Xu
- State Key Laboratory of Plant Physiology and Biochemistry/College of Agronomy and Biotechnology/National Maize Improvement Center/Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, 2 West Yuanmingyuan Road, Beijing, 100193 People’s Republic of China
| | - Tao Zhong
- State Key Laboratory of Plant Physiology and Biochemistry/College of Agronomy and Biotechnology/National Maize Improvement Center/Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, 2 West Yuanmingyuan Road, Beijing, 100193 People’s Republic of China
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138
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Fagny M, Austerlitz F. Polygenic Adaptation: Integrating Population Genetics and Gene Regulatory Networks. Trends Genet 2021; 37:631-638. [PMID: 33892958 DOI: 10.1016/j.tig.2021.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022]
Abstract
The adaptation of populations to local environments often relies on the selection of optimal values for polygenic traits. Here, we first summarize the results obtained from different quantitative genetics and population genetics models, about the genetic architecture of polygenic traits and their response to directional selection. We then highlight the contribution of systems biology to the understanding of the molecular bases of polygenic traits and the evolution of gene regulatory networks involved in these traits. Finally, we discuss the need for a unifying framework merging the fields of population genetics, quantitative genetics and systems biology to better understand the molecular bases of polygenic traits adaptation.
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Affiliation(s)
- Maud Fagny
- UMR7206 Eco-Anthropologie, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Université de Paris, Paris, France.
| | - Frédéric Austerlitz
- UMR7206 Eco-Anthropologie, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Université de Paris, Paris, France
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139
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Chidzanga C, Fleury D, Baumann U, Mullan D, Watanabe S, Kalambettu P, Pontre R, Edwards J, Forrest K, Wong D, Langridge P, Chalmers K, Garcia M. Development of an Australian Bread Wheat Nested Association Mapping Population, a New Genetic Diversity Resource for Breeding under Dry and Hot Climates. Int J Mol Sci 2021; 22:4348. [PMID: 33919411 PMCID: PMC8122485 DOI: 10.3390/ijms22094348] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 12/20/2022] Open
Abstract
Genetic diversity, knowledge of the genetic architecture of the traits of interest and efficient means of transferring the desired genetic diversity into the relevant genetic background are prerequisites for plant breeding. Exotic germplasm is a rich source of genetic diversity; however, they harbor undesirable traits that limit their suitability for modern agriculture. Nested association mapping (NAM) populations are valuable genetic resources that enable incorporation of genetic diversity, dissection of complex traits and providing germplasm to breeding programs. We developed the OzNAM by crossing and backcrossing 73 diverse exotic parents to two Australian elite varieties Gladius and Scout. The NAM parents were genotyped using the iSelect wheat 90K Infinium SNP array, and the progeny were genotyped using a custom targeted genotyping-by-sequencing assay based on molecular inversion probes designed to target 12,179 SNPs chosen from the iSelect wheat 90K Infinium SNP array of the parents. In total, 3535 BC1F4:6 RILs from 125 families with 21 to 76 lines per family were genotyped and we found 4964 polymorphic and multi-allelic haplotype markers that spanned the whole genome. A subset of 530 lines from 28 families were evaluated in multi-environment trials over three years. To demonstrate the utility of the population in QTL mapping, we chose to map QTL for maturity and plant height using the RTM-GWAS approach and we identified novel and known QTL for maturity and plant height.
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Affiliation(s)
- Charity Chidzanga
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064, Australia; (C.C.); (D.F.); (U.B.); (S.W.); (P.K.); (P.L.); (K.C.)
- ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, Waite Research Institute, The University of Adelaide, Glen Osmond, SA 5064, Australia; (D.M.); (J.E.)
| | - Delphine Fleury
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064, Australia; (C.C.); (D.F.); (U.B.); (S.W.); (P.K.); (P.L.); (K.C.)
- ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, Waite Research Institute, The University of Adelaide, Glen Osmond, SA 5064, Australia; (D.M.); (J.E.)
| | - Ute Baumann
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064, Australia; (C.C.); (D.F.); (U.B.); (S.W.); (P.K.); (P.L.); (K.C.)
- ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, Waite Research Institute, The University of Adelaide, Glen Osmond, SA 5064, Australia; (D.M.); (J.E.)
| | - Dan Mullan
- ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, Waite Research Institute, The University of Adelaide, Glen Osmond, SA 5064, Australia; (D.M.); (J.E.)
- Intergrain 19 Ambitious Link, Bibra Lake, WA 6163, Australia;
| | - Sayuri Watanabe
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064, Australia; (C.C.); (D.F.); (U.B.); (S.W.); (P.K.); (P.L.); (K.C.)
- ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, Waite Research Institute, The University of Adelaide, Glen Osmond, SA 5064, Australia; (D.M.); (J.E.)
| | - Priyanka Kalambettu
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064, Australia; (C.C.); (D.F.); (U.B.); (S.W.); (P.K.); (P.L.); (K.C.)
- ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, Waite Research Institute, The University of Adelaide, Glen Osmond, SA 5064, Australia; (D.M.); (J.E.)
| | - Robert Pontre
- Intergrain 19 Ambitious Link, Bibra Lake, WA 6163, Australia;
| | - James Edwards
- ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, Waite Research Institute, The University of Adelaide, Glen Osmond, SA 5064, Australia; (D.M.); (J.E.)
- Australian Grain Technologies, 20 Leitch Rd, Roseworthy, SA 5371, Australia
| | - Kerrie Forrest
- Genomics & Cell Sciences, Agriculture Victoria Research, Department of Jobs, Precincts and Regions, Agribio, 5 Ring Rd, Bundoora, VIC 3083, Australia; (K.F.); (D.W.)
| | - Debbie Wong
- Genomics & Cell Sciences, Agriculture Victoria Research, Department of Jobs, Precincts and Regions, Agribio, 5 Ring Rd, Bundoora, VIC 3083, Australia; (K.F.); (D.W.)
| | - Peter Langridge
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064, Australia; (C.C.); (D.F.); (U.B.); (S.W.); (P.K.); (P.L.); (K.C.)
| | - Ken Chalmers
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064, Australia; (C.C.); (D.F.); (U.B.); (S.W.); (P.K.); (P.L.); (K.C.)
| | - Melissa Garcia
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA 5064, Australia; (C.C.); (D.F.); (U.B.); (S.W.); (P.K.); (P.L.); (K.C.)
- ARC Industrial Transformation Research Hub for Wheat in a Hot and Dry Climate, Waite Research Institute, The University of Adelaide, Glen Osmond, SA 5064, Australia; (D.M.); (J.E.)
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140
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Chen M, Fan W, Ji F, Hua H, Liu J, Yan M, Ma Q, Fan J, Wang Q, Zhang S, Liu G, Sun Z, Tian C, Zhao F, Zheng J, Zhang Q, Chen J, Qiu J, Wei X, Chen Z, Zhang P, Pei D, Yang J, Huang X. Genome-wide identification of agronomically important genes in outcrossing crops using OutcrossSeq. MOLECULAR PLANT 2021; 14:556-570. [PMID: 33429094 DOI: 10.1016/j.molp.2021.01.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/07/2020] [Accepted: 01/06/2021] [Indexed: 05/27/2023]
Abstract
Many important crops (e.g., tuber, root, and tree crops) are cross-pollinating. For these crops, no inbred lines are available for genetic study and breeding because they are self-incompatible, clonally propagated, or have a long generation time, making the identification of agronomically important genes difficult, particularly in crops with a complex autopolyploid genome. In this study, we developed a method, OutcrossSeq, for mapping agronomically important loci in outcrossing crops based on whole-genome low-coverage resequencing of a large genetic population, and designed three computation algorithms in OutcrossSeq for different types of outcrossing populations. We applied OutcrossSeq to a tuberous root crop (sweet potato, autopolyploid), a tree crop (walnut tree, highly heterozygous diploid), and hybrid crops (double-cross populations) to generate high-density genotype maps for the outcrossing populations, which enable precise identification of genomic loci underlying important agronomic traits. Candidate causative genes at these loci were detected based on functional clues. Taken together, our results indicate that OutcrossSeq is a robust and powerful method for identifying agronomically important genes in heterozygous species, including polyploids, in a cost-efficient way. The OutcrossSeq software and its instruction manual are available for downloading at www.xhhuanglab.cn/tool/OutcrossSeq.html.
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Affiliation(s)
- Mengjiao Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Weijuan Fan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Feiyang Ji
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Hua Hua
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jie Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Mengxiao Yan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Qingguo Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Jiongjiong Fan
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Qin Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Shufeng Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Guiling Liu
- Tai'an Academy of Agricultural Sciences, Tai'an 271000, Shandong, China
| | - Zhe Sun
- Tai'an Academy of Agricultural Sciences, Tai'an 271000, Shandong, China
| | - Changgeng Tian
- Tai'an Academy of Agricultural Sciences, Tai'an 271000, Shandong, China
| | - Fengling Zhao
- Tai'an Academy of Agricultural Sciences, Tai'an 271000, Shandong, China
| | - Jianli Zheng
- Tai'an Academy of Agricultural Sciences, Tai'an 271000, Shandong, China
| | - Qi Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jiaxin Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xin Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Ziru Chen
- National Genomics Data Center, Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Peng Zhang
- CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
| | - Dong Pei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China.
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
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141
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Knoch D, Werner CR, Meyer RC, Riewe D, Abbadi A, Lücke S, Snowdon RJ, Altmann T. Multi-omics-based prediction of hybrid performance in canola. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1147-1165. [PMID: 33523261 PMCID: PMC7973648 DOI: 10.1007/s00122-020-03759-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/19/2020] [Indexed: 05/05/2023]
Abstract
Complementing or replacing genetic markers with transcriptomic data and use of reproducing kernel Hilbert space regression based on Gaussian kernels increases hybrid prediction accuracies for complex agronomic traits in canola. In plant breeding, hybrids gained particular importance due to heterosis, the superior performance of offspring compared to their inbred parents. Since the development of new top performing hybrids requires labour-intensive and costly breeding programmes, including testing of large numbers of experimental hybrids, the prediction of hybrid performance is of utmost interest to plant breeders. In this study, we tested the effectiveness of hybrid prediction models in spring-type oilseed rape (Brassica napus L./canola) employing different omics profiles, individually and in combination. To this end, a population of 950 F1 hybrids was evaluated for seed yield and six other agronomically relevant traits in commercial field trials at several locations throughout Europe. A subset of these hybrids was also evaluated in a climatized glasshouse regarding early biomass production. For each of the 477 parental rapeseed lines, 13,201 single nucleotide polymorphisms (SNPs), 154 primary metabolites, and 19,479 transcripts were determined and used as predictive variables. Both, SNP markers and transcripts, effectively predict hybrid performance using (genomic) best linear unbiased prediction models (gBLUP). Compared to models using pure genetic markers, models incorporating transcriptome data resulted in significantly higher prediction accuracies for five out of seven agronomic traits, indicating that transcripts carry important information beyond genomic data. Notably, reproducing kernel Hilbert space regression based on Gaussian kernels significantly exceeded the predictive abilities of gBLUP models for six of the seven agronomic traits, demonstrating its potential for implementation in future canola breeding programmes.
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Affiliation(s)
- Dominic Knoch
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben Germany
| | - Christian R. Werner
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG Scotland, UK
| | - Rhonda C. Meyer
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben Germany
| | - David Riewe
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben Germany
- Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, 14195 Berlin, Germany
| | - Amine Abbadi
- NPZ Innovation GmbH, Hohenlieth, 24363 Holtsee, Germany
- Norddeutsche Pflanzenzucht Hans-Georg Lembke KG, Hohenlieth, 24363 Holtsee, Germany
| | - Sophie Lücke
- Norddeutsche Pflanzenzucht Hans-Georg Lembke KG, Hohenlieth, 24363 Holtsee, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Thomas Altmann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, OT Gatersleben Germany
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142
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Tibbs Cortes L, Zhang Z, Yu J. Status and prospects of genome-wide association studies in plants. THE PLANT GENOME 2021; 14:e20077. [PMID: 33442955 DOI: 10.1002/tpg2.20077] [Citation(s) in RCA: 138] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/18/2020] [Indexed: 05/22/2023]
Abstract
Genome-wide association studies (GWAS) have developed into a powerful and ubiquitous tool for the investigation of complex traits. In large part, this was fueled by advances in genomic technology, enabling us to examine genome-wide genetic variants across diverse genetic materials. The development of the mixed model framework for GWAS dramatically reduced the number of false positives compared with naïve methods. Building on this foundation, many methods have since been developed to increase computational speed or improve statistical power in GWAS. These methods have allowed the detection of genomic variants associated with either traditional agronomic phenotypes or biochemical and molecular phenotypes. In turn, these associations enable applications in gene cloning and in accelerated crop breeding through marker assisted selection or genetic engineering. Current topics of investigation include rare-variant analysis, synthetic associations, optimizing the choice of GWAS model, and utilizing GWAS results to advance knowledge of biological processes. Ongoing research in these areas will facilitate further advances in GWAS methods and their applications.
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Affiliation(s)
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, IA, 50010, USA
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143
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Pujarula V, Pusuluri M, Bollam S, Das RR, Ratnala R, Adapala G, Thuraga V, Rathore A, Srivastava RK, Gupta R. Genetic Variation for Nitrogen Use Efficiency Traits in Global Diversity Panel and Parents of Mapping Populations in Pearl Millet. FRONTIERS IN PLANT SCIENCE 2021; 12:625915. [PMID: 33613608 PMCID: PMC7893144 DOI: 10.3389/fpls.2021.625915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/11/2021] [Indexed: 05/09/2023]
Abstract
Nitrogen (N) is one of the primary macronutrients required for crop growth and yield. This nutrient is especially limiting in the dry and low fertility soils where pearl millet [Pennisetum glaucum (L.) R. Br] is typically grown. Globally, pearl millet is the sixth most important cereal grown by subsistence farmers in the arid and semi-arid regions of sub-Saharan Africa and the Indian subcontinent. Most of these agro-ecologies have low N in the root zone soil strata. Therefore, there is an immense need to identify lines that use nitrogen efficiently. A set of 380 diverse pearl millet lines consisting of a global diversity panel (345), parents of mapping populations (20), and standard checks (15) were evaluated in an alpha-lattice design with two replications, 25 blocks, a three-row plot for 11 nitrogen use efficiency (NUE) related traits across three growing seasons (Summer 2017, Rainy 2017, and Summer 2018) in an N-depleted precision field under three different N levels (0%-N0, 50%-N50, 100%-N100 of recommended N, i.e., 100 kg ha-1). Analysis of variance revealed significant genetic variation for NUE-related traits across treatments and seasons. Nitrogen in limited condition (N0) resulted in a 27.6 and 17.6% reduction in grain yield (GY) and dry stover yield (DSY) compared to N50. Higher reduction in GY and DSY traits by 24.6 and 23.6% were observed under N0 compared to N100. Among the assessed traits, GY exhibited significant positive correlations with nitrogen utilization efficiency (NUtE) and nitrogen harvest index (NHI). This indicated the pivotal role of N remobilization to the grain in enhancing yield levels. Top 25 N-insensitive (NIS-top grain yielders) and N-sensitive (NS-poor grain yielders) genotypes were identified under low N conditions. Out of 25 NIS lines, nine genotypes (IP 10820, IP 17720, ICMB 01222-P1, IP 10379, ICMB 89111-P2, IP 8069, ICMB 90111-P2, ICMV IS89305, and ICMV 221) were common with the top 25 lines for N100 level showing the genotype plasticity toward varying N levels. Low N tolerant genotypes identified from the current investigation may help in the identification of genomic regions responsible for NUE and its deployment in pearl millet breeding programs through marker-assisted selection (MAS).
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Affiliation(s)
| | | | | | | | | | | | | | | | - Rakesh K. Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
| | - Rajeev Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
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144
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Abstract
Birds are one of the most recognizable and diverse groups of organisms on earth. This group has played an important role in many fields, including the development of methods in behavioral ecology and evolutionary theory. The use of population genomics took off following the advent of high-throughput sequencing in various taxa. Several features of avian genomes make them particularly amenable for work in this field, including their nucleated red blood cells permitting easy DNA extraction and small, compact genomes. We review the latest findings in the population genomics of birds here, emphasizing questions related to behavior, ecology, evolution, and conservation. Additionally, we include insights in trait mapping and the ability to obtain accurate estimates of important summary statistics for conservation (e.g., genetic diversity and inbreeding). We highlight roadblocks that will need to be overcome in order to advance work on the population genomics of birds and prospects for future work. Roadblocks include the assembly of more contiguous reference genomes using long-reads and optical mapping. Prospects include the integration of population genomics with additional fields (e.g., landscape genetics, phylogeography, and genomic mapping) along with studies beyond genetic variants (e.g., epigenetics).
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145
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Rey S, Jin X, Damsgård B, Bégout ML, Mackenzie S. Analysis across diverse fish species highlights no conserved transcriptome signature for proactive behaviour. BMC Genomics 2021; 22:33. [PMID: 33413108 PMCID: PMC7792025 DOI: 10.1186/s12864-020-07317-z] [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: 05/12/2020] [Accepted: 12/09/2020] [Indexed: 02/06/2023] Open
Abstract
Background Consistent individual differences in behaviour, known as animal personalities, have been demonstrated within and across species. In fish, studies applying an animal personality approach have been used to resolve variation in physiological and molecular data suggesting a linkage, genotype-phenotype, between behaviour and transcriptome regulation. In this study, using three fish species (zebrafish; Danio rerio, Atlantic salmon; Salmo salar and European sea bass; Dicentrarchus labrax), we firstly address whether personality-specific mRNA transcript abundances are transferrable across distantly-related fish species and secondly whether a proactive transcriptome signature is conserved across all three species. Results Previous zebrafish transcriptome data was used as a foundation to produce a curated list of mRNA transcripts related to animal personality across all three species. mRNA transcript copy numbers for selected gene targets show that differential mRNA transcript abundance in the brain appears to be partially conserved across species relative to personality type. Secondly, we performed RNA-Seq using whole brains from S. salar and D. labrax scoring positively for both behavioural and molecular assays for proactive behaviour. We further enriched this dataset by incorporating a zebrafish brain transcriptome dataset specific to the proactive phenotype. Our results indicate that cross-species molecular signatures related to proactive behaviour are functionally conserved where shared functional pathways suggest that evolutionary convergence may be more important than individual mRNAs. Conclusions Our data supports the proposition that highly polygenic clusters of genes, with small additive effects, likely support the underpinning molecular variation related to the animal personalities in the fish used in this study. The polygenic nature of the proactive brain transcriptome across all three species questions the existence of specific molecular signatures for proactive behaviour, at least at the granularity of specific regulatory gene modules, level of genes, gene networks and molecular functions. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07317-z.
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Affiliation(s)
- Sonia Rey
- Institute of Aquaculture, University of Stirling, Stirlingshire, FK9 4LA, UK
| | - Xingkun Jin
- Institute of Aquaculture, University of Stirling, Stirlingshire, FK9 4LA, UK.,Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, NO-0316, Oslo, Norway.,Institute of Marine Biology, College of Oceanography, Hohai University, Nanjing, 210098, China
| | - Børge Damsgård
- Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, 9037, Tromsø, Norway
| | | | - Simon Mackenzie
- Institute of Aquaculture, University of Stirling, Stirlingshire, FK9 4LA, UK.
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146
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Lin RC, Rausher MD. R2R3-MYB genes control petal pigmentation patterning in Clarkia gracilis ssp. sonomensis (Onagraceae). THE NEW PHYTOLOGIST 2021; 229:1147-1162. [PMID: 32880946 DOI: 10.1111/nph.16908] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 08/20/2020] [Indexed: 06/11/2023]
Abstract
Petal pigmentation patterning is widespread in flowering plants. The genetics of these pattern elements has been of great interest for understanding the evolution of phenotypic diversification. Here, we investigate the genetic changes responsible for the evolution of an unpigmented petal element on a colored background. We used transcriptome analysis, gene expression assays, cosegregation in F2 plants and functional tests to identify the gene(s) involved in petal coloration in Clarkia gracilis ssp. sonomensis. We identified an R2R3-MYB transcription factor (CgsMYB12) responsible for anthocyanin pigmentation of the basal region ('cup') in the petal of C. gracilis ssp. sonomensis. A functional mutation in CgsMYB12 creates a white cup on a pink petal background. Additionally, we found that two R2R3-MYB genes (CgsMYB6 and CgsMYB11) are also involved in petal background pigmentation. Each of these three R2R3-MYB genes exhibits a different spatiotemporal expression pattern. The functionality of these R2R3-MYB genes was confirmed through stable transformation of Arabidopsis. Distinct spatial patterns of R2R3-MYB expression have created the possibility that pigmentation in different sections of the petal can evolve independently. This finding suggests that recent gene duplication has been central to the evolution of petal pigmentation patterning in C. gracilis ssp. sonomensis.
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Affiliation(s)
- Rong-Chien Lin
- Department of Biology, Duke University, Durham, NC, 27708, USA
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Mark D Rausher
- Department of Biology, Duke University, Durham, NC, 27708, USA
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147
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Goldstein I, Ehrenreich IM. The complex role of genetic background in shaping the effects of spontaneous and induced mutations. Yeast 2020; 38:187-196. [PMID: 33125810 PMCID: PMC7984271 DOI: 10.1002/yea.3530] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/09/2020] [Accepted: 10/24/2020] [Indexed: 12/27/2022] Open
Abstract
Spontaneous and induced mutations frequently show different phenotypic effects across genetically distinct individuals. It is generally appreciated that these background effects mainly result from genetic interactions between the mutations and segregating loci. However, the architectures and molecular bases of these genetic interactions are not well understood. Recent work in a number of model organisms has tried to advance knowledge of background effects both by using large‐scale screens to find mutations that exhibit this phenomenon and by identifying the specific loci that are involved. Here, we review this body of research, emphasizing in particular the insights it provides into both the prevalence of background effects across different mutations and the mechanisms that cause these background effects. A large fraction of mutations show different effects in distinct individuals. These background effects are mainly caused by epistasis with segregating loci. Mapping studies show a diversity of genetic architectures can be involved. Genetically complex changes in gene expression are often, but not always, causative.
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Affiliation(s)
- Ilan Goldstein
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089-2910, USA
| | - Ian M Ehrenreich
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California, 90089-2910, USA
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148
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Morgante F, Huang W, Sørensen P, Maltecca C, Mackay TFC. Leveraging Multiple Layers of Data To Predict Drosophila Complex Traits. G3 (BETHESDA, MD.) 2020; 10:4599-4613. [PMID: 33106232 PMCID: PMC7718734 DOI: 10.1534/g3.120.401847] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/12/2020] [Indexed: 02/07/2023]
Abstract
The ability to accurately predict complex trait phenotypes from genetic and genomic data are critical for the implementation of personalized medicine and precision agriculture; however, prediction accuracy for most complex traits is currently low. Here, we used data on whole genome sequences, deep RNA sequencing, and high quality phenotypes for three quantitative traits in the ∼200 inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP) to compare the prediction accuracies of gene expression and genotypes for three complex traits. We found that expression levels (r = 0.28 and 0.38, for females and males, respectively) provided higher prediction accuracy than genotypes (r = 0.07 and 0.15, for females and males, respectively) for starvation resistance, similar prediction accuracy for chill coma recovery (null for both models and sexes), and lower prediction accuracy for startle response (r = 0.15 and 0.14 for female and male genotypes, respectively; and r = 0.12 and 0.11, for females and male transcripts, respectively). Models including both genotype and expression levels did not outperform the best single component model. However, accuracy increased considerably for all the three traits when we included gene ontology (GO) category as an additional layer of information for both genomic variants and transcripts. We found strongly predictive GO terms for each of the three traits, some of which had a clear plausible biological interpretation. For example, for starvation resistance in females, GO:0033500 (r = 0.39 for transcripts) and GO:0032870 (r = 0.40 for transcripts), have been implicated in carbohydrate homeostasis and cellular response to hormone stimulus (including the insulin receptor signaling pathway), respectively. In summary, this study shows that integrating different sources of information improved prediction accuracy and helped elucidate the genetic architecture of three Drosophila complex phenotypes.
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Affiliation(s)
- Fabio Morgante
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695
- Program in Genetics, North Carolina State University, Raleigh, NC 27695
| | - Wen Huang
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695
- Program in Genetics, North Carolina State University, Raleigh, NC 27695
| | - Peter Sørensen
- Center of Quantitative Genetics and Genomics and Department of Molecular Biology and Genetics, Aarhus University, Tjele 8830, Denmark
| | - Christian Maltecca
- Program in Genetics, North Carolina State University, Raleigh, NC 27695
- Department of Animal Science, North Carolina State University, Raleigh, NC 27695
| | - Trudy F C Mackay
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695
- Program in Genetics, North Carolina State University, Raleigh, NC 27695
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149
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Genome wide identification of QTL associated with yield and yield components in two popular wheat cultivars TAM 111 and TAM 112. PLoS One 2020; 15:e0237293. [PMID: 33264303 PMCID: PMC7710072 DOI: 10.1371/journal.pone.0237293] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/10/2020] [Indexed: 12/12/2022] Open
Abstract
Two drought-tolerant wheat cultivars, ‘TAM 111’ and ‘TAM 112’, have been widely grown in the Southern Great Plains of the U.S. and used as parents in many wheat breeding programs worldwide. This study aimed to reveal genetic control of yield and yield components in the two cultivars under both dryland and irrigated conditions. A mapping population containing 124 F5:7 recombinant inbred lines (RILs) was developed from the cross of TAM 112/TAM 111. A set of 5,948 SNPs from the wheat 90K iSelect array and double digest restriction-site associated DNA sequencing was used to construct high-density genetic maps. Data for yield and yield components were obtained from 11 environments. QTL analyses were performed based on 11 individual environments, across all environments, within and across mega-environments. Thirty-six unique consistent QTL regions were distributed on 13 chromosomes including 1A, 1B, 1D, 2A, 2D, 3D, 4B, 4D, 6A, 6B, 6D, 7B, and 7D. Ten unique QTL with pleiotropic effects were identified on four chromosomes and eight were in common with the consistent QTL. These QTL increased dry biomass grain yield by 16.3 g m-2, plot yield by 28.1 g m-2, kernels spike-1 by 0.7, spikes m-2 by 14.8, thousand kernel weight by 0.9 g with favorable alleles from either parent. TAM 112 alleles mainly increased spikes m-2 and thousand kernel weight while TMA 111 alleles increased kernels spike-1, harvest index and grain yield. The saturated genetic map and markers linked to significant QTL from this study will be very useful in developing high throughput genotyping markers for tracking the desirable haplotypes of these important yield-related traits in popular parental cultivars.
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150
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Zhao L, Zhang Z, Rodriguez SMB, Vardarajan BN, Renton AE, Goate AM, Mayeux R, Wang GT, Leal SM. A quantitative trait rare variant nonparametric linkage method with application to age-at-onset of Alzheimer's disease. Eur J Hum Genet 2020; 28:1734-1742. [PMID: 32740652 PMCID: PMC7785016 DOI: 10.1038/s41431-020-0703-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 07/09/2020] [Accepted: 07/22/2020] [Indexed: 12/18/2022] Open
Abstract
To analyze pedigrees with quantitative trait (QT) and sequence data, we developed a rare variant (RV) quantitative nonparametric linkage (QNPL) method, which evaluates sharing of minor alleles. RV-QNPL has greater power than the traditional QNPL that tests for excess sharing of minor and major alleles. RV-QNPL is robust to population substructure and admixture, locus heterogeneity, and inclusion of nonpathogenic variants and can be readily applied outside of coding regions. When QNPL was used to analyze common variants, it often led to loci mapping to large intervals, e.g., >40 Mb. In contrast, when RVs are analyzed, regions are well defined, e.g., a gene. Using simulation studies, we demonstrate that RV-QNPL is substantially more powerful than applying traditional QNPL methods to analyze RVs. RV-QNPL was also applied to analyze age-at-onset (AAO) data for 107 late-onset Alzheimer's disease (LOAD) pedigrees of Caribbean Hispanic and European ancestry with whole-genome sequence data. When AAO of AD was analyzed regardless of APOE ε4 status, suggestive linkage (LOD = 2.4) was observed with RVs in KNDC1 and nominally significant linkage (p < 0.05) was observed with RVs in LOAD genes ABCA7 and IQCK. When AAO of AD was analyzed for APOE ε4 positive family members, nominally significant linkage was observed with RVs in APOE, while when AAO of AD was analyzed for APOE ε4 negative family members, nominal significance was observed for IQCK and ADAMTS1. RV-QNPL provides a powerful resource to analyze QTs in families to elucidate their genetic etiology.
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Affiliation(s)
- Linhai Zhao
- grid.39382.330000 0001 2160 926XCenter for Statistical Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Zhihui Zhang
- grid.39382.330000 0001 2160 926XCenter for Statistical Genetics, Baylor College of Medicine, Houston, TX 77030 USA ,grid.21729.3f0000000419368729Center for Statistical Genetics, Columbia University, New York, NY 10027 USA ,grid.21729.3f0000000419368729Department of Neurology, Taub Institute on Alzheimer’s Disease and the Aging Brain, and Gertrude H. Sergievsky Center, Columbia University, New York, NY 10027 USA
| | - Sandra M. Barral Rodriguez
- grid.21729.3f0000000419368729Department of Neurology, Taub Institute on Alzheimer’s Disease and the Aging Brain, and Gertrude H. Sergievsky Center, Columbia University, New York, NY 10027 USA
| | - Badri N. Vardarajan
- grid.21729.3f0000000419368729Department of Neurology, Taub Institute on Alzheimer’s Disease and the Aging Brain, and Gertrude H. Sergievsky Center, Columbia University, New York, NY 10027 USA
| | - Alan E. Renton
- grid.59734.3c0000 0001 0670 2351Department of Neuroscience and Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Alison M. Goate
- grid.59734.3c0000 0001 0670 2351Department of Neuroscience and Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA ,grid.59734.3c0000 0001 0670 2351Department of Neuroscience and Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY 10029 USA
| | - Richard Mayeux
- grid.21729.3f0000000419368729Department of Neurology, Taub Institute on Alzheimer’s Disease and the Aging Brain, and Gertrude H. Sergievsky Center, Columbia University, New York, NY 10027 USA
| | - Gao T. Wang
- grid.21729.3f0000000419368729Center for Statistical Genetics, Columbia University, New York, NY 10027 USA ,grid.21729.3f0000000419368729Department of Neurology, Taub Institute on Alzheimer’s Disease and the Aging Brain, and Gertrude H. Sergievsky Center, Columbia University, New York, NY 10027 USA ,grid.170205.10000 0004 1936 7822Department of Human Genetics, The University of Chicago, Chicago, IL 60637 USA
| | - Suzanne M. Leal
- grid.39382.330000 0001 2160 926XCenter for Statistical Genetics, Baylor College of Medicine, Houston, TX 77030 USA ,grid.21729.3f0000000419368729Center for Statistical Genetics, Columbia University, New York, NY 10027 USA ,grid.21729.3f0000000419368729Department of Neurology, Taub Institute on Alzheimer’s Disease and the Aging Brain, and Gertrude H. Sergievsky Center, Columbia University, New York, NY 10027 USA
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