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Marone D, Laidò G, Saccomanno A, Petruzzino G, Giaretta Azevedo CV, De Vita P, Mastrangelo AM, Gadaleta A, Ammar K, Bassi FM, Wang M, Chen X, Rubiales D, Matny O, Steffenson BJ, Pecchioni N. Genome-wide association study of common resistance to rust species in tetraploid wheat. FRONTIERS IN PLANT SCIENCE 2024; 14:1290643. [PMID: 38235202 PMCID: PMC10792004 DOI: 10.3389/fpls.2023.1290643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
Rusts of the genus Puccinia are wheat pathogens. Stem (black; Sr), leaf (brown; Lr), and stripe (yellow; Yr) rust, caused by Puccinia graminis f. sp. tritici (Pgt), Puccinia triticina (Pt), and Puccinia striiformis f. sp. tritici (Pst), can occur singularly or in mixed infections and pose a threat to wheat production globally in terms of the wide dispersal of their urediniospores. The development of durable resistant cultivars is the most sustainable method for controlling them. Many resistance genes have been identified, characterized, genetically mapped, and cloned; several quantitative trait loci (QTLs) for resistance have also been described. However, few studies have considered resistance to all three rust pathogens in a given germplasm. A genome-wide association study (GWAS) was carried out to identify loci associated with resistance to the three rusts in a collection of 230 inbred lines of tetraploid wheat (128 of which were Triticum turgidum ssp. durum) genotyped with SNPs. The wheat panel was phenotyped in the field and subjected to growth chamber experiments across different countries (USA, Mexico, Morocco, Italy, and Spain); then, a mixed linear model (MLM) GWAS was performed. In total, 9, 34, and 5 QTLs were identified in the A and B genomes for resistance to Pgt, Pt, and Pst, respectively, at both the seedling and adult plant stages. Only one QTL on chromosome 4A was found to be effective against all three rusts at the seedling stage. Six QTLs conferring resistance to two rust species at the adult plant stage were mapped: three on chromosome 1B and one each on 5B, 7A, and 7B. Fifteen QTLs conferring seedling resistance to two rusts were mapped: five on chromosome 2B, three on 7B, two each on 5B and 6A, and one each on 1B, 2A, and 7A. Most of the QTLs identified were specific for a single rust species or race of a species. Candidate genes were identified within the confidence intervals of a QTL conferring resistance against at least two rust species by using the annotations of the durum (cv. 'Svevo') and wild emmer wheat ('Zavitan') reference genomes. The 22 identified loci conferring resistance to two or three rust species may be useful for breeding new and potentially durable resistant wheat cultivars.
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Affiliation(s)
- Daniela Marone
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Giovanni Laidò
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Antonietta Saccomanno
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Reggio Emilia, Italy
| | - Giuseppe Petruzzino
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Cleber V. Giaretta Azevedo
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Pasquale De Vita
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Anna Maria Mastrangelo
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
| | - Agata Gadaleta
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti (Di.S.S.P.A.), Università di Bari “Aldo Moro”, Bari, Italy
| | - Karim Ammar
- International Maize and Wheat Improvement Centre (CIMMYT), Ciudad de México, Mexico
| | - Filippo M. Bassi
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
- Wheat Health, Genetics, and Quality Research Unit, United States Department of Agriculture - Agriculture Research Service (USDA-ARS), Pullman, WA, United States
| | - Diego Rubiales
- Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (CSIC), Córdoba, Spain
| | - Oadi Matny
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Nicola Pecchioni
- Centro di Ricerca Cerealicoltura e Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Foggia, Italy
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Reggio Emilia, Italy
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Esposito S, Vitale P, Taranto F, Saia S, Pecorella I, D'Agostino N, Rodriguez M, Natoli V, De Vita P. Simultaneous improvement of grain yield and grain protein concentration in durum wheat by using association tests and weighted GBLUP. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:242. [PMID: 37947927 DOI: 10.1007/s00122-023-04487-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
KEY MESSAGE Simultaneous improvement for GY and GPC by using GWAS and GBLUP suggested a significant application in durum wheat breeding. Despite the importance of grain protein concentration (GPC) in determining wheat quality, its negative correlation with grain yield (GY) is still one of the major challenges for breeders. Here, a durum wheat panel of 200 genotypes was evaluated for GY, GPC, and their derived indices (GPD and GYD), under eight different agronomic conditions. The plant material was genotyped with the Illumina 25 k iSelect array, and a genome-wide association study was performed. Two statistical models revealed dozens of marker-trait associations (MTAs), each explaining up to 30%. phenotypic variance. Two markers on chromosomes 2A and 6B were consistently identified by both models and were found to be significantly associated with GY and GPC. MTAs identified for phenological traits co-mapped to well-known genes (i.e., Ppd-1, Vrn-1). The significance values (p-values) that measure the strength of the association of each single nucleotide polymorphism marker with the target traits were used to perform genomic prediction by using a weighted genomic best linear unbiased prediction model. The trained models were ultimately used to predict the agronomic performances of an independent durum wheat panel, confirming the utility of genomic prediction, although environmental conditions and genetic backgrounds may still be a challenge to overcome. The results generated through our study confirmed the utility of GPD and GYD to mitigate the inverse GY and GPC relationship in wheat, provided novel markers for marker-assisted selection and opened new ways to develop cultivars through genomic prediction approaches.
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Affiliation(s)
- Salvatore Esposito
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA - Council for Agricultural Research and Economics, SS 673 Meters 25200, 71122, Foggia, Italy
| | - Paolo Vitale
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA - Council for Agricultural Research and Economics, SS 673 Meters 25200, 71122, Foggia, Italy
- Department of Agriculture, Food, Natural Science, Engineering, University of Foggia, Via Napoli 25, 71122, Foggia, Italy
| | - Francesca Taranto
- Institute of Biosciences and Bioresources (CNR-IBBR), Via Amendola 165/A, 70126, Bari, Italy
| | - Sergio Saia
- Department of Veterinary Sciences, University of Pisa, 56129, Pisa, Italy
| | - Ivano Pecorella
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA - Council for Agricultural Research and Economics, SS 673 Meters 25200, 71122, Foggia, Italy
| | - Nunzio D'Agostino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Monica Rodriguez
- Department of Agriculture, University of Sassari, Viale Italia, 39, 07100, Sassari, Italy
| | - Vincenzo Natoli
- Genetic Services SRL, Contrada Catenaccio, snc, 71026, Deliceto, FG, Italy
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA - Council for Agricultural Research and Economics, SS 673 Meters 25200, 71122, Foggia, Italy.
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Wharrie S, Yang Z, Raj V, Monti R, Gupta R, Wang Y, Martin A, O’Connor LJ, Kaski S, Marttinen P, Palamara PF, Lippert C, Ganna A. HAPNEST: efficient, large-scale generation and evaluation of synthetic datasets for genotypes and phenotypes. Bioinformatics 2023; 39:btad535. [PMID: 37647640 PMCID: PMC10493177 DOI: 10.1093/bioinformatics/btad535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 08/23/2023] [Accepted: 08/29/2023] [Indexed: 09/01/2023] Open
Abstract
MOTIVATION Existing methods for simulating synthetic genotype and phenotype datasets have limited scalability, constraining their usability for large-scale analyses. Moreover, a systematic approach for evaluating synthetic data quality and a benchmark synthetic dataset for developing and evaluating methods for polygenic risk scores are lacking. RESULTS We present HAPNEST, a novel approach for efficiently generating diverse individual-level genotypic and phenotypic data. In comparison to alternative methods, HAPNEST shows faster computational speed and a lower degree of relatedness with reference panels, while generating datasets that preserve key statistical properties of real data. These desirable synthetic data properties enabled us to generate 6.8 million common variants and nine phenotypes with varying degrees of heritability and polygenicity across 1 million individuals. We demonstrate how HAPNEST can facilitate biobank-scale analyses through the comparison of seven methods to generate polygenic risk scoring across multiple ancestry groups and different genetic architectures. AVAILABILITY AND IMPLEMENTATION A synthetic dataset of 1 008 000 individuals and nine traits for 6.8 million common variants is available at https://www.ebi.ac.uk/biostudies/studies/S-BSST936. The HAPNEST software for generating synthetic datasets is available as Docker/Singularity containers and open source Julia and C code at https://github.com/intervene-EU-H2020/synthetic_data.
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Affiliation(s)
- Sophie Wharrie
- Department of Computer Science, Aalto University, Espoo 02150, Finland
| | - Zhiyu Yang
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Vishnu Raj
- Department of Computer Science, Aalto University, Espoo 02150, Finland
| | - Remo Monti
- Hasso Plattner Institute, University of Potsdam, Digital Engineering Faculty, Potsdam 14469, Germany
| | - Rahul Gupta
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Ying Wang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Alicia Martin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Luke J O’Connor
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Samuel Kaski
- Department of Computer Science, Aalto University, Espoo 02150, Finland
- Department of Computer Science, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Pekka Marttinen
- Department of Computer Science, Aalto University, Espoo 02150, Finland
| | | | - Christoph Lippert
- Hasso Plattner Institute, University of Potsdam, Digital Engineering Faculty, Potsdam 14469, Germany
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York 10065, United States
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki 00014, Finland
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
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Mulugeta B, Ortiz R, Geleta M, Hailesilassie T, Hammenhag C, Hailu F, Tesfaye K. Harnessing genome-wide genetic diversity, population structure and linkage disequilibrium in Ethiopian durum wheat gene pool. FRONTIERS IN PLANT SCIENCE 2023; 14:1192356. [PMID: 37546270 PMCID: PMC10400094 DOI: 10.3389/fpls.2023.1192356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/05/2023] [Indexed: 08/08/2023]
Abstract
Yanyang Liu, Henan Academy of Agricultural Sciences (HNAAS), China; Landraces are an important genetic source for transferring valuable novel genes and alleles required to enhance genetic variation. Therefore, information on the gene pool's genetic diversity and population structure is essential for the conservation and sustainable use of durum wheat genetic resources. Hence, the aim of this study was to assess genetic diversity, population structure, and linkage disequilibrium, as well as to identify regions with selection signature. Five hundred (500) individuals representing 46 landraces, along with 28 cultivars were evaluated using the Illumina Infinium 25K wheat SNP array, resulting in 8,178 SNPs for further analysis. Gene diversity (GD) and the polymorphic information content (PIC) ranged from 0.13-0.50 and 0.12-0.38, with mean GD and PIC values of 0.34 and 0.27, respectively. Linkage disequilibrium (LD) revealed 353,600 pairs of significant SNPs at a cut-off (r2 > 0.20, P < 0.01), with an average r2 of 0.21 for marker pairs. The nucleotide diversity (π) and Tajima's D (TD) per chromosome for the populations ranged from 0.29-0.36 and 3.46-5.06, respectively, with genome level, mean π values of 0.33 and TD values of 4.43. Genomic scan using the Fst outlier test revealed 85 loci under selection signatures, with 65 loci under balancing selection and 17 under directional selection. Putative candidate genes co-localized with regions exhibiting strong selection signatures were associated with grain yield, plant height, host plant resistance to pathogens, heading date, grain quality, and phenolic content. The Bayesian Model (STRUCTURE) and distance-based (principal coordinate analysis, PCoA, and unweighted pair group method with arithmetic mean, UPGMA) methods grouped the genotypes into five subpopulations, where landraces from geographically non-adjoining environments were clustered in the same cluster. This research provides further insights into population structure and genetic relationships in a diverse set of durum wheat germplasm, which could be further used in wheat breeding programs to address production challenges sustainably.
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Affiliation(s)
- Behailu Mulugeta
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
- Sinana Agricultural Research Center, Oromia Agricultural Research Institute, Bale-Robe, Ethiopia
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Faris Hailu
- Bio and Emerging Technology Institute, Addis Ababa, Ethiopia
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Biology and Biotechnology, Wollo University, Dessie, Ethiopia
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Amponsah Adjei E, Esuma W, Alicai T, Bhattacharjee R, Dramadri IO, Edema R, Chamba EB, Odong TL. Genetic diversity and population structure of Uganda's yam (Dioscorea spp.) genetic resource based on DArTseq. PLoS One 2023; 18:e0277537. [PMID: 36787288 PMCID: PMC9928066 DOI: 10.1371/journal.pone.0277537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 10/31/2022] [Indexed: 02/15/2023] Open
Abstract
Assessing the genetic diversity of yam germplasm from different geographical origins for cultivation and breeding purposes is an essential step for crop genetic resource conservation and genetic improvement, especially where the crop faces minimal attention. This study aimed to classify the population structure, and assess the extent of genetic diversity in 207 Dioscorea rotundata genotypes sourced from three different geographical origins. A total of 4,957 (16.2%) single nucleotide polymorphism markers were used to assess genetic diversity. The SNP markers were informative, with polymorphic information content ranging from 0.238 to 0.288 and a mean of 0.260 across all the genotypes. The observed and expected heterozygosity was 0.12 and 0.23, respectively while the minor allele frequency ranged from 0.093 to 0.124 with a mean of 0.109. The principal coordinate analysis, model-based structure and discriminant analysis of principal components, and the Euclidean distance matrix method grouped 207 yam genotypes into three main clusters. Genotypes from West Africa (Ghana and Nigeria) had significant similarities with those from Uganda. Analysis of molecular variance revealed that within-population variation across three different geographical origins accounted for 93% of the observed variation. This study, therefore, showed that yam improvement in Uganda is possible, and the outcome will constitute a foundation for the genetic improvement of yams in Uganda.
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Affiliation(s)
- Emmanuel Amponsah Adjei
- Department of Agricultural Production, Makerere University, Kampala, Uganda
- Makerere University Regional Center for Crop Improvement, Makerere University, Kampala, Uganda
- Council for Scientific and Industrial Research—Savanna Agricultural Research Institute, Kumasi, Ghana
- * E-mail:
| | - Williams Esuma
- National Crops Resources Research Institute, Kampala, Uganda
| | - Titus Alicai
- National Crops Resources Research Institute, Kampala, Uganda
| | | | - Isaac Onziga Dramadri
- Department of Agricultural Production, Makerere University, Kampala, Uganda
- Makerere University Regional Center for Crop Improvement, Makerere University, Kampala, Uganda
| | - Richard Edema
- Department of Agricultural Production, Makerere University, Kampala, Uganda
- Makerere University Regional Center for Crop Improvement, Makerere University, Kampala, Uganda
| | - Emmanuel Boache Chamba
- Council for Scientific and Industrial Research—Savanna Agricultural Research Institute, Kumasi, Ghana
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Rabieyan E, Bihamta MR, Moghaddam ME, Mohammadi V, Alipour H. Genome-wide association mapping and genomic prediction of agronomical traits and breeding values in Iranian wheat under rain-fed and well-watered conditions. BMC Genomics 2022; 23:831. [PMID: 36522726 PMCID: PMC9753272 DOI: 10.1186/s12864-022-08968-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 10/26/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The markers detected by genome-wide association study (GWAS) make it possible to dissect genetic structure and diversity at many loci. This can enable a wheat breeder to reveal and used genomic loci controlling drought tolerance. This study was focused on determining the population structure of Iranian 208 wheat landraces and 90 cultivars via genotyping-by-sequencing (GBS) and also on detecting marker-trait associations (MTAs) by GWAS and genomic prediction (GS) of wheat agronomic traits for drought-tolerance breeding. GWASs were conducted using both the original phenotypes (pGWAS) and estimated breeding values (eGWAS). The bayesian ridge regression (BRR), genomic best linear unbiased prediction (gBLUP), and ridge regression-best linear unbiased prediction (rrBLUP) approaches were used to estimate breeding values and estimate prediction accuracies in genomic selection. RESULTS Population structure analysis using 2,174,975 SNPs revealed four genetically distinct sub-populations from wheat accessions. D-Genome harbored the lowest number of significant marker pairs and the highest linkage disequilibrium (LD), reflecting different evolutionary histories of wheat genomes. From pGWAS, BRR, gBLUP, and rrBLUP, 284, 363, 359 and 295 significant MTAs were found under normal and 195, 365, 362 and 302 under stress conditions, respectively. The gBLUP with the most similarity (80.98 and 71.28% in well-watered and rain-fed environments, correspondingly) with the pGWAS method in the terms of discovered significant SNPs, suggesting the potential of gBLUP in uncovering SNPs. Results from gene ontology revealed that 29 and 30 SNPs in the imputed dataset were located in protein-coding regions for well-watered and rain-fed conditions, respectively. gBLUP model revealed genetic effects better than other models, suggesting a suitable tool for genome selection in wheat. CONCLUSION We illustrate that Iranian landraces of bread wheat contain novel alleles that are adaptive to drought stress environments. gBLUP model can be helpful for fine mapping and cloning of the relevant QTLs and genes, and for carrying out trait introgression and marker-assisted selection in both normal and drought environments in wheat collections.
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Affiliation(s)
- Ehsan Rabieyan
- grid.46072.370000 0004 0612 7950Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
| | - Mohammad Reza Bihamta
- grid.46072.370000 0004 0612 7950Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
| | | | - Valiollah Mohammadi
- grid.46072.370000 0004 0612 7950Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
| | - Hadi Alipour
- grid.412763.50000 0004 0442 8645Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran
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Ro N, Haile M, Kim B, Cho GT, Lee J, Lee YJ, Hyun DY. Genome-Wide Association Study for Agro-Morphological Traits in Eggplant Core Collection. PLANTS (BASEL, SWITZERLAND) 2022; 11:2627. [PMID: 36235493 PMCID: PMC9571982 DOI: 10.3390/plants11192627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/01/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Eggplant is one of the most economically and nutritionally important vegetables worldwide. The study of the association of phenotypic traits with genetic factors is vital for the rapid and efficient identification and selection of eggplant genetic resources for breeding purposes with desired traits. The eggplant resources (587) collected from different countries, including Korea, were used for establishing the core collection. A total of 288 accessions were selected from 587 Solanum accessions based on 52 single nucleotide polymorphisms (SNPs) markers together with 17 morphological traits. This core collection was further used to analyze the genetic associations of eggplant morphological variations. A large variation was found among the evaluated eggplant accessions for some agro-morphological traits. Stem prickles and leaf prickles showed a significant positive correlation (r = 0.83***), followed by days to flowering and days to maturity (r = 0.64***). A total of 114,981 SNPs were filtered and used for phylogenetic tree analysis, population structure analysis, and genome-wide association study (GWAS). Among the agro-morphological traits, significantly associated SNPs were found for six traits. A total of 377 significantly associated SNPs with six agro-morphological traits were identified. These six traits and the number of SNPs were: days to maturity (51), flower size (121), fruit width (20), harvest fruit color (42), leaf prickles (38), and stem prickles (105). The largest fraction of significant SNPs (11.94%) was obtained on chromosome Ch01, followed by Ch07 and Ch06 with 11.67% and 10.08%, respectively. This study will help to develop markers linked to the most important agro-morphological traits of eggplant genetic resources and support the selection of desirable traits for eggplant breeding programs.
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Affiliation(s)
- Nayoung Ro
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Mesfin Haile
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Bichsaem Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Gyu-Taek Cho
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Jungro Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Yoon-Jung Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Do Yoon Hyun
- Department of Crops and Forestry, Korea National University of Agriculture and Fisheries, Jeonju 54874, Korea;
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Genievskaya Y, Pecchioni N, Laidò G, Anuarbek S, Rsaliyev A, Chudinov V, Zatybekov A, Turuspekov Y, Abugalieva S. Genome-Wide Association Study of Leaf Rust and Stem Rust Seedling and Adult Resistances in Tetraploid Wheat Accessions Harvested in Kazakhstan. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11151904. [PMID: 35893608 PMCID: PMC9329756 DOI: 10.3390/plants11151904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/13/2022] [Accepted: 07/20/2022] [Indexed: 05/05/2023]
Abstract
Leaf rust (LR) and stem rust (SR) are diseases increasingly impacting wheat production worldwide. Fungal pathogens producing rust diseases in wheat may cause yield losses of up to 50−60%. One of the most effective methods for preventing such losses is the development of resistant cultivars with high yield potential. This goal can be achieved through complex breeding studies, including the identification of key genetic factors controlling rust disease resistance. The objective of this study was to identify sources of tetraploid wheat resistance to LR and SR races, both at the seedling growth stage in the greenhouse and at the adult plant stage in field experiments, under the conditions of the North Kazakhstan region. A panel consisting of 193 tetraploid wheat accessions was used in a genome-wide association study (GWAS) for the identification of quantitative trait loci (QTLs) associated with LR and SR resistance, using 16,425 polymorphic single-nucleotide polymorphism (SNP) markers in the seedling and adult stages of plant development. The investigated panel consisted of seven tetraploid subspecies (Triticum turgidum ssp. durum, ssp. turanicum, ssp. turgidum, ssp. polonicum, ssp. carthlicum, ssp. dicoccum, and ssp. dicoccoides). The GWAS, based on the phenotypic evaluation of the tetraploid collection’s reaction to the two rust species at the seedling (in the greenhouse) and adult (in the field) stages, revealed 38 QTLs (p < 0.001), comprising 17 for LR resistance and 21 for SR resistance. Ten QTLs were associated with the reaction to LR at the seedling stage, while six QTLs were at the adult plant stage and one QTL was at both the seedling and adult stages. Eleven QTLs were associated with SR response at the seedling stage, while nine QTLs were at the adult plant stage and one QTL was at both the seedling and adult stages. A comparison of these results with previous LR and SR studies indicated that 11 of the 38 QTLs are presumably novel loci. The QTLs identified in this work can potentially be used for marker-assisted selection of tetraploid and hexaploid wheat for the breeding of new LR- and SR-resistant cultivars.
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Affiliation(s)
- Yuliya Genievskaya
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (Y.G.); (S.A.); (A.Z.); (Y.T.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Nicola Pecchioni
- Research Centre for Cereal and Industrial Crops, 71122 Foggia, Italy; (N.P.); (G.L.)
| | - Giovanni Laidò
- Research Centre for Cereal and Industrial Crops, 71122 Foggia, Italy; (N.P.); (G.L.)
| | - Shynar Anuarbek
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (Y.G.); (S.A.); (A.Z.); (Y.T.)
| | - Aralbek Rsaliyev
- Laboratory of Phytosanitary Safety, Research Institute of Biological Safety Problems, Gvardeisky 080409, Kazakhstan;
| | - Vladimir Chudinov
- Breeding Department, Karabalyk Agricultural Experimental Station, Nauchnoe 110908, Kazakhstan;
| | - Alibek Zatybekov
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (Y.G.); (S.A.); (A.Z.); (Y.T.)
| | - Yerlan Turuspekov
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (Y.G.); (S.A.); (A.Z.); (Y.T.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Saule Abugalieva
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (Y.G.); (S.A.); (A.Z.); (Y.T.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
- Correspondence: ; Tel.: +7-727-394-8006
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Alkemade JA, Nazzicari N, Messmer MM, Annicchiarico P, Ferrari B, Voegele RT, Finckh MR, Arncken C, Hohmann P. Genome-wide association study reveals white lupin candidate gene involved in anthracnose resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1011-1024. [PMID: 34988630 PMCID: PMC8942938 DOI: 10.1007/s00122-021-04014-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 12/06/2021] [Indexed: 05/11/2023]
Abstract
GWAS identifies candidate gene controlling resistance to anthracnose disease in white lupin. White lupin (Lupinus albus L.) is a promising grain legume to meet the growing demand for plant-based protein. Its cultivation, however, is severely threatened by anthracnose disease caused by the fungal pathogen Colletotrichum lupini. To dissect the genetic architecture for anthracnose resistance, genotyping by sequencing was performed on white lupin accessions collected from the center of domestication and traditional cultivation regions. GBS resulted in 4611 high-quality single-nucleotide polymorphisms (SNPs) for 181 accessions, which were combined with resistance data observed under controlled conditions to perform a genome-wide association study (GWAS). Obtained disease phenotypes were shown to highly correlate with overall three-year disease assessments under Swiss field conditions (r > 0.8). GWAS results identified two significant SNPs associated with anthracnose resistance on gene Lalb_Chr05_g0216161 encoding a RING zinc-finger E3 ubiquitin ligase which is potentially involved in plant immunity. Population analysis showed a remarkably fast linkage disequilibrium decay, weak population structure and grouping of commercial varieties with landraces, corresponding to the slow domestication history and scarcity of modern breeding efforts in white lupin. Together with 15 highly resistant accessions identified in the resistance assay, our findings show promise for further crop improvement. This study provides the basis for marker-assisted selection, genomic prediction and studies aimed at understanding anthracnose resistance mechanisms in white lupin and contributes to improving breeding programs worldwide.
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Affiliation(s)
- Joris A Alkemade
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Nelson Nazzicari
- Research Centre for Animal Production and Aquaculture, CREA, Lodi, Italy
| | - Monika M Messmer
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland.
| | | | - Barbara Ferrari
- Research Centre for Animal Production and Aquaculture, CREA, Lodi, Italy
| | - Ralf T Voegele
- Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Maria R Finckh
- Department of Ecological Plant Protection, University of Kassel, Witzenhausen, Germany
| | - Christine Arncken
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Pierre Hohmann
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
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Nutritional improvement of cereal crops to combat hidden hunger during COVID-19 pandemic: Progress and prospects. ADVANCES IN FOOD SECURITY AND SUSTAINABILITY 2022. [PMCID: PMC8917837 DOI: 10.1016/bs.af2s.2022.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
COVID-19 has posed a severe challenge on food security by limiting access to food for the marginally placed population. While access to food is a challenge, access to nutritional food is a greater challenge to the population. The present-day foods are not sufficient to meet the nutritional requirements of the human body. In a pandemic condition, providing nutritious food to the population is imperative to ensure the health and well-being of humankind. Exploiting the existing biodiversity of crop species and deploying classical and modern tools to improve the nutritional potential of these species holds the key to addressing the above challenge. Breeding has been a classical tool of crop improvement that relied predominantly on genetic diversity. Collecting and conserving diverse germplasms and characterizing their diversity using molecular markers is essential to preserve diversity and use them in genetic improvement programs. These markers are also valuable for association mapping analyses to identify the genetic determinants of traits-of-interest in crop species. Association mapping identifies the quantitative trait loci (QTL) underlying the trait-of-interest by exploring marker-trait associations, and these QTLs can further be exploited for the genetic improvement of cultivated species through genomics-assisted breeding. Conventional breeding and genomics approaches are also being applied to develop biofortified cereal crops to reduce nutritional deficiencies in consumers. In this context, chapter explains the prerequisites for association mapping, population structure, genetic diversity, different approaches of performing association mapping to dissect nutritional traits, use the information for genomics-assisted breeding for nutrient-rich cereal crops, and application of genomics strategies in crop biofortification. These approaches will ensure food and nutrition security for all amidst the current COVID-19 crisis.
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11
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Sodedji FAK, Agbahoungba S, Agoyi EE, Kafoutchoni MK, Choi J, Nguetta SPA, Assogbadjo AE, Kim HY. Diversity, population structure, and linkage disequilibrium among cowpea accessions. THE PLANT GENOME 2021; 14:e20113. [PMID: 34275189 DOI: 10.1002/tpg2.20113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/03/2021] [Indexed: 05/27/2023]
Abstract
Cowpea [Vigna unguiculata (L.) Walp] is a globally important food security crop. However, it is susceptible to pest and disease; hence, constant breeding efforts based on its diversity are required for its improvement. The present study aims to investigate the genetic diversity, population structure, and linkage disequilibrium (LD) among 274 cowpea accessions from different origins. A total of 3,127 single nucleotide polymorphism (SNP) markers generated using diversity array technology (DArT) was used. Population structure, neighbor-joining clustering, and principal component analyses indicated three subpopulations within the germplasm. Results of STRUCTURE analysis and discriminant analysis of principal components (DAPC) were complementary in assessing the structuration of the diversity among the germplasm, with the grouping of the accessions improved in DAPC. Genetic distances of 0.005-0.44 were observed among accessions. Accessions from western and central Africa, eastern and central Africa, and Asia were predominant and distributed across all subpopulations. The subpopulations had fixation indexes of 0.48-0.56. Analysis of molecular variance revealed that within subpopulation variation accounted for 81% of observed genetic variation in the germplasm. The subpopulations mainly consisted of inbred lines (inbreeding coefficient = 1) with common alleles, although they were from different geographical regions. This reflects considerable seed movement and germplasm exchange between regions. The LD was characterized by low decay for great physical distances between markers. The LD decay distance varied among chromosomes with the average distance of 80-100 kb across the genome. Thus, crop improvement is possible, and the LD will facilitate genome-wide association studies on quality attributes and critical agronomic traits in cowpea.
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Affiliation(s)
- Frejus Ariel Kpedetin Sodedji
- Smart Farm Research Center, Korea Institute of Science and Technology (KIST), Gangneung, Gangwon, 25451, Republic of Korea
- Non-timber Forest Products and Orphan Crop Species Unit, Laboratory of Applied Ecology (LEA), University of Abomey-Calavi (UAC), 01 BP: 526 Cotonou, Benin
- West Africa Center of Excellence in Climate Change Biodiversity and Sustainable Agriculture (CEA-CCBAD), Biosciences Research Unit, University Felix Houphouet-Boigny, Abidjan, Lagunes, 22 BP 461, Côte d'Ivoire
| | - Symphorien Agbahoungba
- Smart Farm Research Center, Korea Institute of Science and Technology (KIST), Gangneung, Gangwon, 25451, Republic of Korea
| | - Eric Echikintho Agoyi
- Non-timber Forest Products and Orphan Crop Species Unit, Laboratory of Applied Ecology (LEA), University of Abomey-Calavi (UAC), 01 BP: 526 Cotonou, Benin
| | - Médard Konoutan Kafoutchoni
- Non-timber Forest Products and Orphan Crop Species Unit, Laboratory of Applied Ecology (LEA), University of Abomey-Calavi (UAC), 01 BP: 526 Cotonou, Benin
| | - Jaeyoung Choi
- Smart Farm Research Center, Korea Institute of Science and Technology (KIST), Gangneung, Gangwon, 25451, Republic of Korea
| | - Simon-Pierre Assanvo Nguetta
- West Africa Center of Excellence in Climate Change Biodiversity and Sustainable Agriculture (CEA-CCBAD), Biosciences Research Unit, University Felix Houphouet-Boigny, Abidjan, Lagunes, 22 BP 461, Côte d'Ivoire
| | - Achille Ephrem Assogbadjo
- Smart Farm Research Center, Korea Institute of Science and Technology (KIST), Gangneung, Gangwon, 25451, Republic of Korea
| | - Ho-Youn Kim
- Non-timber Forest Products and Orphan Crop Species Unit, Laboratory of Applied Ecology (LEA), University of Abomey-Calavi (UAC), 01 BP: 526 Cotonou, Benin
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12
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Roncallo PF, Larsen AO, Achilli AL, Pierre CS, Gallo CA, Dreisigacker S, Echenique V. Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes. BMC Genomics 2021; 22:233. [PMID: 33820546 PMCID: PMC8022437 DOI: 10.1186/s12864-021-07519-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 03/02/2021] [Indexed: 01/04/2023] Open
Abstract
Background Durum wheat (Triticum turgidum L. ssp. durum Desf. Husn) is the main staple crop used to make pasta products worldwide. Under the current climate change scenarios, genetic variability within a crop plays a crucial role in the successful release of new varieties with high yields and wide crop adaptation. In this study we evaluated a durum wheat collection consisting of 197 genotypes that mainly comprised a historical set of Argentinian germplasm but also included worldwide accessions. Results We assessed the genetic diversity, population structure and linkage disequilibrium (LD) patterns in this collection using a 35 K SNP array. The level of polymorphism was considered, taking account of the frequent and rare allelic variants. A total of 1547 polymorphic SNPs was located within annotated genes. Genetic diversity in the germplasm collection increased slightly from 1915 to 2010. However, a reduction in genetic diversity using SNPs with rare allelic variants was observed after 1979. However, larger numbers of rare private alleles were observed in the 2000–2009 period, indicating that a high reservoir of rare alleles is still present among the recent germplasm in a very low frequency. The percentage of pairwise loci in LD in the durum genome was low (13.4%) in our collection. Overall LD and the high (r2 > 0.7) or complete (r2 = 1) LD presented different patterns in the chromosomes. The LD increased over three main breeding periods (1915–1979, 1980–1999 and 2000–2020). Conclusions Our results suggest that breeding and selection have impacted differently on the A and B genomes, particularly on chromosome 6A and 2A. The collection was structured in five sub-populations and modern Argentinian accessions (cluster Q4) which were clearly differentiated. Our study contributes to the understanding of the complexity of Argentinian durum wheat germplasm and to derive future breeding strategies enhancing the use of genetic diversity in a more efficient and targeted way. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07519-z.
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Affiliation(s)
- Pablo Federico Roncallo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Departamento de Agronomía, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Adelina Olga Larsen
- CEI Barrow, Instituto Nacional de Tecnología Agropecuaria (INTA), Tres Arroyos, Buenos Aires, Argentina
| | - Ana Laura Achilli
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Departamento de Agronomía, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Carolina Saint Pierre
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Edo. de México, Mexico
| | - Cristian Andrés Gallo
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Departamento de Agronomía, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Susanne Dreisigacker
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Edo. de México, Mexico
| | - Viviana Echenique
- Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS), Departamento de Agronomía, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina.
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13
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Colasuonno P, Marcotuli I, Gadaleta A, Soriano JM. From Genetic Maps to QTL Cloning: An Overview for Durum Wheat. PLANTS (BASEL, SWITZERLAND) 2021; 10:315. [PMID: 33562160 PMCID: PMC7914919 DOI: 10.3390/plants10020315] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/26/2021] [Accepted: 02/02/2021] [Indexed: 12/17/2022]
Abstract
Durum wheat is one of the most important cultivated cereal crops, providing nutrients to humans and domestic animals. Durum breeding programs prioritize the improvement of its main agronomic traits; however, the majority of these traits involve complex characteristics with a quantitative inheritance (quantitative trait loci, QTL). This can be solved with the use of genetic maps, new molecular markers, phenotyping data of segregating populations, and increased accessibility to sequences from next-generation sequencing (NGS) technologies. This allows for high-density genetic maps to be developed for localizing candidate loci within a few Kb in a complex genome, such as durum wheat. Here, we review the identified QTL, fine mapping, and cloning of QTL or candidate genes involved in the main traits regarding the quality and biotic and abiotic stresses of durum wheat. The current knowledge on the used molecular markers, sequence data, and how they changed the development of genetic maps and the characterization of QTL is summarized. A deeper understanding of the trait architecture useful in accelerating durum wheat breeding programs is envisioned.
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Affiliation(s)
- Pasqualina Colasuonno
- Department of Agricultural and Environmental Science, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A, 70126 Bari, Italy; (P.C.); (I.M.)
| | - Ilaria Marcotuli
- Department of Agricultural and Environmental Science, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A, 70126 Bari, Italy; (P.C.); (I.M.)
| | - Agata Gadaleta
- Department of Agricultural and Environmental Science, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A, 70126 Bari, Italy; (P.C.); (I.M.)
| | - Jose Miguel Soriano
- Sustainable Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), 25198 Lleida, Spain
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14
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Di Guardo M, Farneti B, Khomenko I, Modica G, Mosca A, Distefano G, Bianco L, Troggio M, Sottile F, La Malfa S, Biasioli F, Gentile A. Genetic characterization of an almond germplasm collection and volatilome profiling of raw and roasted kernels. HORTICULTURE RESEARCH 2021; 8:27. [PMID: 33518710 PMCID: PMC7848010 DOI: 10.1038/s41438-021-00465-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/11/2020] [Accepted: 12/17/2020] [Indexed: 05/16/2023]
Abstract
Almond is appreciated for its nutraceutical value and for the aromatic profile of the kernels. In this work, an almond collection composed of 96 Sicilian accessions complemented with 10 widely cultivated cultivars was phenotyped for the production of volatile organic compounds using a proton-transfer time-of-flight mass spectrometer and genotyped using the Illumina Infinium®18 K Peach SNP array. The profiling of the aroma was carried out on fresh and roasted kernels enabling the detection of 150 mass peaks. Sixty eight, for the most related with sulfur compounds, furan containing compounds, and aldehydes formed by Strecker degradation, significantly increased during roasting, while the concentration of fifty-four mass peaks, for the most belonging to alcohols and terpenes, significantly decreased. Four hundred and seventy-one robust SNPs were selected and employed for population genetic studies. Structure analysis detected three subpopulations with the Sicilian accessions characterized by a different genetic stratification compared to those collected in Apulia (South Italy) and the International cultivars. The linkage-disequilibrium (LD) decay across the genome was equal to r2 = 0.083. Furthermore, a high level of collinearity (r2 = 0.96) between almond and peach was registered confirming the high synteny between the two genomes. A preliminary application of a genome-wide association analysis allowed the detection of significant marker-trait associations for 31 fresh and 33 roasted almond mass peaks respectively. An accurate genetic and phenotypic characterization of novel germplasm can represent a valuable tool for the set-up of marker-assisted selection of novel cultivars with an enhanced aromatic profile.
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Affiliation(s)
- M Di Guardo
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123, Catania, Italy
| | - B Farneti
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all' Adige, Trento, Italy
| | - I Khomenko
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all' Adige, Trento, Italy
| | - G Modica
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123, Catania, Italy
| | - A Mosca
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123, Catania, Italy
| | - G Distefano
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123, Catania, Italy.
| | - L Bianco
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all' Adige, Trento, Italy
| | - M Troggio
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all' Adige, Trento, Italy
| | - F Sottile
- Dipartimento di Architettura, University of Palermo, Viale delle Scienze, Ed. 14 90128, Palermo, Italy
| | - S La Malfa
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123, Catania, Italy
| | - F Biasioli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all' Adige, Trento, Italy
| | - A Gentile
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123, Catania, Italy
- National Center for Citrus Improvement, College of Horticulture and Landscape, Hunan Agricultural University, Changsha, China
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15
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Combination of Linkage Mapping, GWAS, and GP to Dissect the Genetic Basis of Common Rust Resistance in Tropical Maize Germplasm. Int J Mol Sci 2020; 21:ijms21186518. [PMID: 32899999 PMCID: PMC7555316 DOI: 10.3390/ijms21186518] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/01/2020] [Accepted: 09/04/2020] [Indexed: 12/27/2022] Open
Abstract
Common rust (CR) caused by Puccina sorghi is one of the destructive fungal foliar diseases of maize and has been reported to cause moderate to high yield losses. Providing CR resistant germplasm has the potential to increase yields. To dissect the genetic architecture of CR resistance in maize, association mapping, in conjunction with linkage mapping, joint linkage association mapping (JLAM), and genomic prediction (GP) was conducted on an association-mapping panel and five F3 biparental populations using genotyping-by-sequencing (GBS) single-nucleotide polymorphisms (SNPs). Analysis of variance for the biparental populations and the association panel showed significant genotypic and genotype x environment (GXE) interaction variances except for GXE of Pop4. Heritability (h2) estimates were moderate with 0.37-0.45 for the individual F3 populations, 0.45 across five populations and 0.65 for the association panel. Genome-wide association study (GWAS) analyses revealed 14 significant marker-trait associations which individually explained 6-10% of the total phenotypic variances. Individual population-based linkage analysis revealed 26 QTLs associated with CR resistance and together explained 14-40% of the total phenotypic variances. Linkage mapping revealed seven QTLs in pop1, nine QTL in pop2, four QTL in pop3, five QTL in pop4, and one QTL in pop5, distributed on all chromosomes except chromosome 10. JLAM for the 921 F3 families from five populations detected 18 QTLs distributed in all chromosomes except on chromosome 8. These QTLs individually explained 0.3 to 3.1% and together explained 45% of the total phenotypic variance. Among the 18 QTL detected through JLAM, six QTLs, qCR1-78, qCR1-227, qCR3-172, qCR3-186, qCR4-171, and qCR7-137 were also detected in linkage mapping. GP within population revealed low to moderate correlations with a range from 0.19 to 0.51. Prediction correlation was high with r = 0.78 for combined analysis of the five F3 populations. Prediction of biparental populations by using association panel as training set reveals positive correlations ranging from 0.05 to 0.22, which encourages to develop an independent but related population as a training set which can be used to predict diverse but related populations. The findings of this study provide valuable information on understanding the genetic basis of CR resistance and the obtained information can be used for developing functional molecular markers for marker-assisted selection and for implementing GP to improve CR resistance in tropical maize.
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16
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Anuarbek S, Abugalieva S, Pecchioni N, Laidò G, Maccaferri M, Tuberosa R, Turuspekov Y. Quantitative trait loci for agronomic traits in tetraploid wheat for enhancing grain yield in Kazakhstan environments. PLoS One 2020; 15:e0234863. [PMID: 32574201 PMCID: PMC7310741 DOI: 10.1371/journal.pone.0234863] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/03/2020] [Indexed: 12/02/2022] Open
Abstract
Durum wheat (Triticum turgidum L. ssp. durum) is one of the top crops in Kazakhstan, where it is cultivated in different ecological niches, mainly at higher latitudes in the steppe zone of the northern region. Therefore, local breeding programs for durum wheat are primarily focused on selection for high productivity in Northern Kazakhstan based on the introduction of promising foreign germplasm and the adoption of marker-assisted selection. In this study, a world tetraploid wheat collection consisted of 184 primitive and domesticated accessions, which were previously genotyped using 16,425 polymorphic SNP markers, was field-tested in Northern and South-eastern Kazakhstan. The field tests have allowed the identification of 80 durum wheat promising lines in Northern Kazakhstan in comparison with a local standard cultivar. Also, GGE (Genotype and Genotype by Environment) biplot analyses for yield performance revealed that accessions of T. dicoccum, T. carthlicum, and T. turanicum also have potential to improve durum wheat yield in the region. The genome-wide association study (GWAS) has allowed the identification of 83 MTAs (marker-trait associations) for heading date, seed maturation time, plant height, spike length, number of fertile spikes, number of kernels per spike, and thousand kernel weight. The comparison of the 83 identified MTAs with those previously reported in GWAS for durum wheat suggests that 38 MTAs are presumably novel, while the co-localization of a large number of MTAs with those previously published confirms the validity of the results of this study. The MTAs reported herewith will provide the opportunity to implement marker-assisted selection in ongoing durum wheat breeding projects targeting higher productivity in the region.
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Affiliation(s)
- Shynar Anuarbek
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Saule Abugalieva
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- Kazakh National Agrarian University, Almaty, Kazakhstan
| | - Nicola Pecchioni
- Research Centre for Cereal and Industrial Crops, CREA, Foggia, Italy
| | - Giovanni Laidò
- Research Centre for Cereal and Industrial Crops, CREA, Foggia, Italy
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Yerlan Turuspekov
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
- al-Farabi Kazakh National University, Almaty, Kazakhstan
- * E-mail:
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17
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Potential of Genome-Wide Association Studies and Genomic Selection to Improve Productivity and Quality of Commercial Timber Species in Tropical Rainforest, a Case Study of Shorea platyclados. FORESTS 2020. [DOI: 10.3390/f11020239] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Shorea platyclados (Dark Red Meranti) is a commercially important timber tree species in Southeast Asia. However, its stocks have dramatically declined due, inter alia, to excessive logging, insufficient natural regeneration and a slow recovery rate. Thus, there is a need to promote enrichment planting and develop effective technique to support its rehabilitation and improve timber production through implementation of Genome-Wide Association Studies (GWAS) and Genomic Selection (GS). To assist such efforts, plant materials were collected from a half-sib progeny population in Sari Bumi Kusuma forest concession, Kalimantan, Indonesia. Using 5900 markers in sequences obtained from 356 individuals, we detected high linkage disequilibrium (LD) extending up to >145 kb, suggesting that associations between phenotypic traits and markers in LD can be more easily and feasibly detected with GWAS than with analysis of quantitative trait loci (QTLs). However, the detection power of GWAS seems low, since few single nucleotide polymorphisms linked to any focal traits were detected with a stringent false discovery rate, indicating that the species’ phenotypic traits are mostly under polygenic quantitative control. Furthermore, Machine Learning provided higher prediction accuracies than Bayesian methods. We also found that stem diameter, branch diameter ratio and wood density were more predictable than height, clear bole, branch angle and wood stiffness traits. Our study suggests that GS has potential for improving the productivity and quality of S. platyclados, and our genomic heritability estimates may improve the selection of traits to target in future breeding of this species.
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18
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Mahboubi M, Mehrabi R, Naji AM, Talebi R. Whole-genome diversity, population structure and linkage disequilibrium analysis of globally diverse wheat genotypes using genotyping-by-sequencing DArTseq platform. 3 Biotech 2020; 10:48. [PMID: 32002339 PMCID: PMC6960278 DOI: 10.1007/s13205-019-2014-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 12/08/2019] [Indexed: 02/03/2023] Open
Abstract
In this study, 129 wheat genotypes from globally diverse origins were genotyped using DArTseq (SilicoDArT and SNP) markers. After filtering markers for quality-filtering, 14,270 SilicoDArTs and 6484 SNPs were retained and used for genetic diversity, population structure and linkage disequilibrium analyses. The highest number of SilicoDArT and SNP markers mapped on genome A and B compared to genome D. In both marker types, polymorphism information content (PIC) values ranged from 0.1 to 0.5, while > 0.80% of SilicoDArTs and > 0.44% SNPs showed PIC value more than median (0.25%). Un-weighted Neighbor Joining cluster analysis and Bayesian-based model population structure grouped wheat genotypes into three and four clusters, respectively. Principal component analysis and discriminant analysis of principal component results showed highly match with cluster and population structure analysis. Linkage disequilibrium (LD) was more extensive in both marker types, while graphical display of LD decay for both marker types showed that LD declined in the region close to 15 kbp, where r 2-values corresponded to r 2 = 0.16. Overall, our genetic diversity analysis showed high level of variation in studied wheat genotypes, even though there was no relationship between wheat grouping and origins. This might be attributed to admixture level that occurred during long-term natural selection of wheat genotypes in different parts of the world. Highly diverse wheat genotypes used in this study may possess unique genes and are useful sources in breeding programs to improve grain yield and quality.
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Affiliation(s)
- Mojgan Mahboubi
- College of Agriculture, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
| | - Rahim Mehrabi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, PO Box 8415683111, Isfahan, Iran
| | - Amir Mohammad Naji
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahed University, Tehran, Iran
| | - Reza Talebi
- College of Agriculture, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
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Marone D, Rodriguez M, Saia S, Papa R, Rau D, Pecorella I, Laidò G, Pecchioni N, Lafferty J, Rapp M, Longin FH, De Vita P. Genome-Wide Association Mapping of Prostrate/Erect Growth Habit in Winter Durum Wheat. Int J Mol Sci 2020; 21:ijms21020394. [PMID: 31936286 PMCID: PMC7014441 DOI: 10.3390/ijms21020394] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/28/2019] [Accepted: 01/06/2020] [Indexed: 02/08/2023] Open
Abstract
By selecting for prostrate growth habit of the juvenile phase of the cycle, durum wheat cultivars could be developed with improved competitive ability against weeds, and better soil coverage to reduce the soil water lost by evaporation. A panel of 184 durum wheat (Triticum turgidum subsp. durum) genotypes, previously genotyped with DArT-seq markers, was used to perform association mapping analysis of prostrate/erect growth habit trait and to identify candidate genes. Phenotypic data of plant growth habit were recorded during three consecutive growing seasons (2014–2016), two different growth conditions (field trial and greenhouse) and two sowing periods (autumn and spring). Genome-wide association study revealed significant marker-trait associations, twelve of which were specific for a single environment/year, 4 consistent in two environments, and two MTAs for the LSmeans were identified across all environments, on chromosomes 2B and 5A. The co-localization of some MTAs identified in this study with known vernalization and photoperiod genes demonstrated that the sensitivity to vernalization and photoperiod response are actually not only key components of spring/winter growth habit, but they play also an important role in defining the magnitude of the tiller angle during the tillering stage. Many zinc-finger transcription factors, such as C2H2 or CCCH-domain zinc finger proteins, known to be involved in plant growth habit and in leaf angle regulation were found as among the most likely candidate genes. The highest numbers of candidate genes putatively related to the trait were found on chromosomes 3A, 4B, 5A and 6A. Moreover, a bioinformatic approach has been considered to search for functional ortholog genes in wheat by using the sequence of rice and barley tiller angle-related genes. The information generated could be used to improve the understanding of the mechanisms that regulate the prostrate/erect growth habit in wheat and the adaptive potential of durum wheat under resource-limited environmental conditions.
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Affiliation(s)
- Daniela Marone
- Research Centre for Cereal and Industrial Crops, CREA, SS 673, km 25.200, 71122 Foggia, Italy; (D.M.); (S.S.); (I.P.); (G.L.); (N.P.)
| | - Monica Rodriguez
- Department of Agriculture, University of Sassari, Via E. de Nicola, 14, 07100 Sassari, Italy; (M.R.); (D.R.)
- Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale, Università degli Studi di Sassari, SS 127bis, km 28.500 Surigheddu, 07041 Alghero, Italy
| | - Sergio Saia
- Research Centre for Cereal and Industrial Crops, CREA, SS 673, km 25.200, 71122 Foggia, Italy; (D.M.); (S.S.); (I.P.); (G.L.); (N.P.)
- Research Centre for Cereal and Industrial Crops, CREA, SS 11, km 2.500, 13100 Vercelli, Italy
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy;
| | - Domenico Rau
- Department of Agriculture, University of Sassari, Via E. de Nicola, 14, 07100 Sassari, Italy; (M.R.); (D.R.)
| | - Ivano Pecorella
- Research Centre for Cereal and Industrial Crops, CREA, SS 673, km 25.200, 71122 Foggia, Italy; (D.M.); (S.S.); (I.P.); (G.L.); (N.P.)
| | - Giovanni Laidò
- Research Centre for Cereal and Industrial Crops, CREA, SS 673, km 25.200, 71122 Foggia, Italy; (D.M.); (S.S.); (I.P.); (G.L.); (N.P.)
| | - Nicola Pecchioni
- Research Centre for Cereal and Industrial Crops, CREA, SS 673, km 25.200, 71122 Foggia, Italy; (D.M.); (S.S.); (I.P.); (G.L.); (N.P.)
| | - Julia Lafferty
- Saatzucht Donau GesmbH & CoKG, Saatzuchtstrasse 11, A-2301 Probstdorf, Austria;
| | - Matthias Rapp
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstraße 21, 70593 Stuttgart, Germany; (M.R.); (F.H.L.)
| | - Friedrich H. Longin
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstraße 21, 70593 Stuttgart, Germany; (M.R.); (F.H.L.)
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops, CREA, SS 673, km 25.200, 71122 Foggia, Italy; (D.M.); (S.S.); (I.P.); (G.L.); (N.P.)
- Correspondence: ; Tel.: +39-0881-714911
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20
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Rufo R, Alvaro F, Royo C, Soriano JM. From landraces to improved cultivars: Assessment of genetic diversity and population structure of Mediterranean wheat using SNP markers. PLoS One 2019; 14:e0219867. [PMID: 31306459 PMCID: PMC6629082 DOI: 10.1371/journal.pone.0219867] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 07/02/2019] [Indexed: 11/18/2022] Open
Abstract
Assessment of genetic diversity and population structure in crops is essential for breeding and germplasm conservation. A collection of 354 bread wheat genotypes, including Mediterranean landraces and modern cultivars representative of the ones most widely grown in the Mediterranean Basin, were characterized with 11196 single nucleotide polymorphism (SNP) markers. Total genetic diversity (HT) and polymorphic information content (PIC) were 0.36 and 0.30 respectively for both landraces and modern cultivars. Linkage disequilibrium for the modern cultivars was higher than for the landraces (0.18 and 0.12, respectively). Analysis of the genetic structure showed a clear geographical pattern for the landraces, which were clustered into three subpopulations (SPs) representing the western, northern and eastern Mediterranean, whereas the modern cultivars were structured according to the breeding programmes that developed them: CIMMYT/ICARDA, France/Italy, and Balkan/eastern European countries. The modern cultivars showed higher genetic differentiation (GST) and lower gene flow (0.1673 and 2.49, respectively) than the landraces (0.1198 and 3.67, respectively), indicating a better distinction between subpopulations. The maximum gene flow was observed between landraces from the northern Mediterranean SPs and the modern cultivars released mainly by French and Italian breeding programmes.
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Affiliation(s)
- Rubén Rufo
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
| | - Fanny Alvaro
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
| | - Conxita Royo
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
| | - Jose Miguel Soriano
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
- * E-mail:
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21
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Roncallo PF, Beaufort V, Larsen AO, Dreisigacker S, Echenique V. Genetic diversity and linkage disequilibrium using SNP (KASP) and AFLP markers in a worldwide durum wheat (Triticum turgidum L. var durum) collection. PLoS One 2019; 14:e0218562. [PMID: 31251752 PMCID: PMC6741835 DOI: 10.1371/journal.pone.0218562] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/04/2019] [Indexed: 11/18/2022] Open
Abstract
The aim of this work was to analyze the genetic diversity and linkage disequilibrium in a collection of 168 durum wheat accessions (Triticum turgidum L. var. durum) of different origins. Our collection was mainly composed of released and unreleased Argentinian germplasm, with additional genotypes from Italy, Chile, France, CIMMYT, Cyprus, USA and WANA region. To this end, the entire collection was characterized with 85 Single Nucleotide Polymorphism (SNP) markers obtained by Kompetitive Allele Specific PCR (KASP), giving a heterozygosity (He) mean value of 0.183 and a coefficient of genetic differentiation (Gst) value of 0.139. A subset of 119 accessions was characterized with six Amplified Fragment Length Polymorphism (AFLP) primer combinations. A total of 181 polymorphic markers (125 AFLP and 56 SNP) amplified across this subset revealed He measures of 0.352 and 0.182, respectively. Of these, 134 were selected to estimate the genome-wide linkage disequilibrium obtaining low significant values (r2 = 0.11) in the subset, indicating its suitability for future genome-wide association studies (GWAS). The structure analysis conducted in the entire collection with SNP detected two subpopulations. However, the structure analysis conducted with AFLP markers in the subset of 119 accessions proved to have greater degree of resolution and detect six subpopulations. The information provided by both marker types was complementary and showed a strong association between old Argentinian and Italian germplasm and a contribution of CIMMYT germplasm to modern Argentinian, Chilean and Cypriot accessions. The influence of Mediterranean germplasm, mainly from Italy, on part of the modern Argentinian cultivars or breeding lines was also clearly evidenced. Although our analysis yields conclusive results and useful information for association mapping studies, further analyses are needed to refine the number of subpopulations present in the germplasm collection analyzed.
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Affiliation(s)
- Pablo Federico Roncallo
- Centro de Recursos Naturales Renovables de la Zona Semiárida
(CERZOS–CCT–CONICET Bahía Blanca) and Departamento de Agronomía, Universidad
Nacional del Sur, Bahía Blanca, Argentina
| | - Valeria Beaufort
- Centro de Recursos Naturales Renovables de la Zona Semiárida
(CERZOS–CCT–CONICET Bahía Blanca) and Departamento de Agronomía, Universidad
Nacional del Sur, Bahía Blanca, Argentina
| | - Adelina Olga Larsen
- CEI Barrow, Instituto Nacional de Tecnología Agropecuaria (INTA), Tres
Arroyos, Buenos Aires, Argentina
| | - Susanne Dreisigacker
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Edo.
de México, México
| | - Viviana Echenique
- Centro de Recursos Naturales Renovables de la Zona Semiárida
(CERZOS–CCT–CONICET Bahía Blanca) and Departamento de Agronomía, Universidad
Nacional del Sur, Bahía Blanca, Argentina
- * E-mail:
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22
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Nigro D, Gadaleta A, Mangini G, Colasuonno P, Marcotuli I, Giancaspro A, Giove SL, Simeone R, Blanco A. Candidate genes and genome-wide association study of grain protein content and protein deviation in durum wheat. PLANTA 2019; 249:1157-1175. [PMID: 30603787 DOI: 10.1007/s00425-018-03075-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 12/19/2018] [Indexed: 05/26/2023]
Abstract
Stable QTL for grain protein content co-migrating with nitrogen-related genes have been identified by the candidate genes and genome-wide association mapping approaches useful for marker-assisted selection. Grain protein content (GPC) is one of the most important quality traits in wheat, defining the nutritional and end-use properties and rheological characteristics. Over the years, a number of breeding programs have been developed aimed to improving GPC, most of them having been prevented by the negative correlation with grain yield. To overcome this issue, a collection of durum wheat germplasm was evaluated for both GPC and grain protein deviation (GPD) in seven field trials. Fourteen candidate genes involved in several processes related to nitrogen metabolism were precisely located on two high-density consensus maps of common and durum wheat, and six of them were found to be highly associated with both traits. The wheat collection was genotyped using the 90 K iSelect array, and 11 stable quantitative trait loci (QTL) for GPC were detected in at least three environments and the mean across environments by the genome-wide association mapping. Interestingly, seven QTL were co-migrating with N-related candidate genes. Four QTL were found to be significantly associated to increases of GPD, indicating that selecting for GPC could not affect final grain yield per spike. The combined approaches of candidate genes and genome-wide association mapping led to a better understanding of the genetic relationships between grain storage proteins and grain yield per spike, and provided useful information for marker-assisted selection programs.
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Affiliation(s)
- D Nigro
- Department of Soil, Plant and Food Sciences, Genetics and Plant Breeding Section, University of Bari, Bari, Italy
| | - A Gadaleta
- Department of Agricultural and Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, Bari, Italy.
| | - G Mangini
- Department of Soil, Plant and Food Sciences, Genetics and Plant Breeding Section, University of Bari, Bari, Italy
| | - P Colasuonno
- Department of Agricultural and Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, Bari, Italy
| | - I Marcotuli
- Department of Agricultural and Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, Bari, Italy
| | - A Giancaspro
- Department of Agricultural and Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, Bari, Italy
| | - S L Giove
- Department of Agricultural and Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, Bari, Italy
| | - R Simeone
- Department of Soil, Plant and Food Sciences, Genetics and Plant Breeding Section, University of Bari, Bari, Italy
| | - A Blanco
- Department of Soil, Plant and Food Sciences, Genetics and Plant Breeding Section, University of Bari, Bari, Italy
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23
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Maldonado C, Mora F, Scapim CA, Coan M. Genome-wide haplotype-based association analysis of key traits of plant lodging and architecture of maize identifies major determinants for leaf angle: hapLA4. PLoS One 2019; 14:e0212925. [PMID: 30840677 PMCID: PMC6402688 DOI: 10.1371/journal.pone.0212925] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 02/12/2019] [Indexed: 11/18/2022] Open
Abstract
Traits related to plant lodging and architecture are important determinants of plant productivity in intensive maize cultivation systems. Motivated by the identification of genomic associations with the leaf angle, plant height (PH), ear height (EH) and the EH/PH ratio, we characterized approximately 7,800 haplotypes from a set of high-quality single nucleotide polymorphisms (SNPs), in an association panel consisting of tropical maize inbred lines. The proportion of the phenotypic variations explained by the individual SNPs varied between 7%, for the SNP S1_285330124 (located on chromosome 9 and associated with the EH/PH ratio), and 22%, for the SNP S1_317085830 (located on chromosome 6 and associated with the leaf angle). A total of 40 haplotype blocks were significantly associated with the traits of interest, explaining up to 29% of the phenotypic variation for the leaf angle, corresponding to the haplotype hapLA4.04, which was stable over two growing seasons. Overall, the associations for PH, EH and the EH/PH ratio were environment-specific, which was confirmed by performing a model comparison analysis using the information criteria of Akaike and Schwarz. In addition, five stable haplotypes (83%) and 15 SNPs (75%) were identified for the leaf angle. Finally, approximately 62% of the associated haplotypes (25/40) did not contain SNPs detected in the association study using individual SNP markers. This result confirms the advantage of haplotype-based genome-wide association studies for examining genomic regions that control the determining traits for architecture and lodging in maize plants.
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Affiliation(s)
- Carlos Maldonado
- Institute of Biological Sciences, University of Talca, Talca, Chile
| | - Freddy Mora
- Institute of Biological Sciences, University of Talca, Talca, Chile
| | - Carlos A. Scapim
- Universidade Estadual de Maringá, Departamento de Agronomia, Maringá, PR, Brazil
| | - Marlon Coan
- Universidade Estadual de Maringá, Departamento de Agronomia, Maringá, PR, Brazil
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Saccomanno A, Matny O, Marone D, Laidò G, Petruzzino G, Mazzucotelli E, Desiderio F, Blanco A, Gadaleta A, Pecchioni N, De Vita P, Steffenson B, Mastrangelo AM. Genetic Mapping of Loci for Resistance to Stem Rust in a Tetraploid Wheat Collection. Int J Mol Sci 2018; 19:E3907. [PMID: 30563213 PMCID: PMC6321032 DOI: 10.3390/ijms19123907] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/04/2018] [Accepted: 12/04/2018] [Indexed: 01/31/2023] Open
Abstract
Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a major biotic constraint to wheat production worldwide. Disease resistant cultivars are a sustainable means for the efficient control of this disease. To identify quantitative trait loci (QTLs) conferring resistance to stem rust at the seedling stage, an association mapping panel consisting of 230 tetraploid wheat accessions were evaluated for reaction to five Pgt races under greenhouse conditions. A high level of phenotypic variation was observed in the panel in response to all of the races, allowing for genome-wide association mapping of resistance QTLs in wild, landrace, and cultivated tetraploid wheats. Twenty-two resistance QTLs were identified, which were characterized by at least two marker-trait associations. Most of the identified resistance loci were coincident with previously identified rust resistance genes/QTLs; however, six regions detected on chromosomes 1B, 5A, 5B, 6B, and 7B may be novel. Availability of the reference genome sequence of wild emmer wheat accession Zavitan facilitated the search for candidate resistance genes in the regions where QTLs were identified, and many of them were annotated as NOD (nucleotide binding oligomerization domain)-like receptor (NLR) genes or genes related to broad spectrum resistance.
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Affiliation(s)
- Antonietta Saccomanno
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia (FG), Italy.
| | - Oadi Matny
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA.
| | - Daniela Marone
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia (FG), Italy.
| | - Giovanni Laidò
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia (FG), Italy.
| | - Giuseppe Petruzzino
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia (FG), Italy.
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinfomatics, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Francesca Desiderio
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinfomatics, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Antonio Blanco
- Department of Agricultural & Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, 70126 Bari, Italy.
| | - Agata Gadaleta
- Department of Agricultural & Environmental Science, Research Unit of "Genetics and Plant Biotechnology", University of Bari, 70126 Bari, Italy.
| | - Nicola Pecchioni
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia (FG), Italy.
| | - Pasquale De Vita
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia (FG), Italy.
| | - Brian Steffenson
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA.
| | - Anna Maria Mastrangelo
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 24126 Bergamo (BG), Italy.
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Fayaz F, Aghaee Sarbarzeh M, Talebi R, Azadi A. Genetic Diversity and Molecular Characterization of Iranian Durum Wheat Landraces (Triticum turgidum durum (Desf.) Husn.) Using DArT Markers. Biochem Genet 2018; 57:98-116. [PMID: 30051349 DOI: 10.1007/s10528-018-9877-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 07/14/2018] [Indexed: 01/07/2023]
Abstract
Durum wheat is grown mainly in rain-fed regions of Iran and the Mediterranean district under stressful conditions. Different environmental conditions and agricultural practices among ancient communities have led to the development of locally adapted genotypes known as landraces. Landraces are a valued source of genetic variety and show definite adaptation to local environmental conditions according to their home of origin. This study aimed to explore linkage disequilibrium (LD) analysis and the population structure and genetic diversity of Iranian durum wheat landraces. In this study, population structure and genome-wide LD were investigated in 129 durum landrace accessions using 1500 DArT markers. Both structure and discriminant analysis of principal components obviously subdivided the sample collection into seven distinct groups centered on key ancestors and regions of origin of the germplasm. Genetic diversity among the populations was primarily within population (68 vs. 32%). Mean LD values across the entire population sample decayed below r2 of 0.11 after 1 cM. LD decay of genomes A and B of Iranian durum wheat landrace is approximately 2-3 cM (r2 = 0.11) and approximately 0.5 cM (r2 = 0.12), respectively. Altogether, low LD decay, a high number of subpopulations, and the high existence of genetic diversity among and within populations were characteristics of the Iranian durum landrace collection. Hence, the existing genetic diversity within the population can be associated with the very long evolutionary history of plants in Iran. The populations we studied are hence presented as a valuable resource that can be used in basic and applied research in durum wheat breeding.
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Affiliation(s)
- Farzad Fayaz
- Department of Agronomy & Plant Breeding, College of Agriculture, Islamic Azad University, Sanandaj Branch, Sanandaj, Iran.
| | - Mostafa Aghaee Sarbarzeh
- Seed and Plant Improvement Institute, Agriculture Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Reza Talebi
- Department of Agronomy & Plant Breeding, College of Agriculture, Islamic Azad University, Sanandaj Branch, Sanandaj, Iran
| | - Amin Azadi
- Department of Plant Breeding, Yadegar-e-Imam Khomeini (RAH), Islamic Azad University, Shahre Rey Branch, Tehran, Iran
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Ayana GT, Ali S, Sidhu JS, Gonzalez Hernandez JL, Turnipseed B, Sehgal SK. Genome-Wide Association Study for Spot Blotch Resistance in Hard Winter Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:926. [PMID: 30034404 PMCID: PMC6043670 DOI: 10.3389/fpls.2018.00926] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/11/2018] [Indexed: 05/06/2023]
Abstract
Spot blotch (SB) caused by Cochliobolus sativus (anamorph: Bipolaris sorokiniana) is an economically important disease of wheat worldwide. Under a severe epidemic condition, the disease can cause yield losses up to 70%. Previous approaches like bi-parental mapping for identifying SB resistant genes/QTLs exploited only a limited portion of the available genetic diversity with a lower capacity to detect polygenic traits, and had a lower marker density. In this study, we performed genome-wide association study (GWAS) for SB resistance in hard winter wheat association mapping panel (HWWAMP) of 294 genotypes. The HWWAMP was evaluated for response to B. sorokiniana (isolate SD40), and a range of reactions was observed with 10 resistant, 38 moderately resistant, 120 moderately resistant- moderately susceptible, 111 moderately susceptible, and 15 susceptible genotypes. GWAS using 15,590 high-quality SNPs and 294 genotypes we identified six QTLs (p = <0.001) on chromosomes 2D, 3A, 4A, 4B, 5A, and 7B that collectively explained 30% of the total variation for SB resistance. Highly associated SNPs were identified for all six QTLs, QSb.sdsu-2D.1 (SNP: Kukri_c31121_1460, R2 = 4%), QSb.sdsu-3A.1 (SNP: Excalibur_c46082_440, R2 = 4%), QSb.sdsu-4A.1 (SNP: IWA8475, R2 = 5.5%), QSb.sdsu-4B.1 (SNP: Excalibur_rep_c79414_306, R2 = 4%), QSb.sdsu-5A.1 (SNP: Kukri_rep_c104877_2166, R2 = 6%), and QSb.sdsu-7B.1 (SNP: TA005844-0160, R2 = 6%). Our study not only validates three (2D, 5A, and 7B) genomic regions identified in previous studies but also provides highly associated SNP markers for marker assisted selection. In addition, we identified three novel QTLs (QSb.sdsu-3A.1, QSb.sdsu-4A.1, and QSb.sdsu-4B.1) for SB resistance in wheat. Gene annotation analysis of the candidate regions identified nine NBS-LRR and 38 other plant defense-related protein families across multiple QTLs, and these could be used for fine mapping and further characterization of SB resistance in wheat. Comparative analysis with barley indicated the SB resistance locus on wheat chromosomes 2D, 3A, 5A, and 7B identified in our study are syntenic to the previously identified SB resistance locus on chromosomes 2H, 3H, 5H, and 7H in barley. The 10 highly resistant genotypes and SNP markers identified in our study could be very useful resources for breeding of SB resistance in wheat.
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Affiliation(s)
| | | | | | | | | | - Sunish K. Sehgal
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
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27
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Mangini G, Gadaleta A, Colasuonno P, Marcotuli I, Signorile AM, Simeone R, De Vita P, Mastrangelo AM, Laidò G, Pecchioni N, Blanco A. Genetic dissection of the relationships between grain yield components by genome-wide association mapping in a collection of tetraploid wheats. PLoS One 2018; 13:e0190162. [PMID: 29324803 PMCID: PMC5764242 DOI: 10.1371/journal.pone.0190162] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/09/2017] [Indexed: 11/29/2022] Open
Abstract
Increasing grain yield potential in wheat has been a major target of most breeding programs. Genetic advance has been frequently hindered by negative correlations among yield components that have been often observed in segregant populations and germplasm collections. A tetraploid wheat collection was evaluated in seven environments and genotyped with a 90K SNP assay to identify major and stable quantitative trait loci (QTL) for grain yield per spike (GYS), kernel number per spike (KNS) and thousand-kernel weight (TKW), and to analyse the genetic relationships between the yield components at QTL level. The genome-wide association analysis detected eight, eleven and ten QTL for KNS, TKW and GYS, respectively, significant in at least three environments or two environments and the mean across environments. Most of the QTL for TKW and KNS were found located in different marker intervals, indicating that they are genetically controlled independently by each other. Out of eight KNS QTL, three were associated to significant increases of GYS, while the increased grain number of five additional QTL was completely or partially compensated by decreases in grain weight, thus producing no or reduced effects on GYS. Similarly, four consistent and five suggestive TKW QTL resulted in visible increase of GYS, while seven additional QTL were associated to reduced effects in grain number and no effects on GYS. Our results showed that QTL analysis for detecting TKW or KNS alleles useful for improving grain yield potential should consider the pleiotropic effects of the QTL or the association to other QTLs.
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Affiliation(s)
- Giacomo Mangini
- Department of Soil, Plant & Food Sciences, Genetics and Plant Breeding Section, University Aldo Moro, Bari, Italy
| | - Agata Gadaleta
- Department of Agricultural & Environmental Science, Research Unit of “Genetics and Plant Biotechnology”, University Aldo Moro, Bari, Italy
- * E-mail:
| | - Pasqualina Colasuonno
- Department of Agricultural & Environmental Science, Research Unit of “Genetics and Plant Biotechnology”, University Aldo Moro, Bari, Italy
| | - Ilaria Marcotuli
- Department of Agricultural & Environmental Science, Research Unit of “Genetics and Plant Biotechnology”, University Aldo Moro, Bari, Italy
| | - Antonio M. Signorile
- Department of Soil, Plant & Food Sciences, Genetics and Plant Breeding Section, University Aldo Moro, Bari, Italy
| | - Rosanna Simeone
- Department of Soil, Plant & Food Sciences, Genetics and Plant Breeding Section, University Aldo Moro, Bari, Italy
| | - Pasquale De Vita
- Council for Agricultural Research and Economics—Cereal Research Centre, Foggia, Italy
| | - Anna M. Mastrangelo
- Council for Agricultural Research and Economics—Cereal Research Centre, Foggia, Italy
| | - Giovanni Laidò
- Council for Agricultural Research and Economics—Cereal Research Centre, Foggia, Italy
| | - Nicola Pecchioni
- Council for Agricultural Research and Economics—Cereal Research Centre, Foggia, Italy
| | - Antonio Blanco
- Department of Soil, Plant & Food Sciences, Genetics and Plant Breeding Section, University Aldo Moro, Bari, Italy
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Ayana GT, Ali S, Sidhu JS, Gonzalez Hernandez JL, Turnipseed B, Sehgal SK. Genome-Wide Association Study for Spot Blotch Resistance in Hard Winter Wheat. FRONTIERS IN PLANT SCIENCE 2018. [PMID: 30034404 DOI: 10.3389/fpls00926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Spot blotch (SB) caused by Cochliobolus sativus (anamorph: Bipolaris sorokiniana) is an economically important disease of wheat worldwide. Under a severe epidemic condition, the disease can cause yield losses up to 70%. Previous approaches like bi-parental mapping for identifying SB resistant genes/QTLs exploited only a limited portion of the available genetic diversity with a lower capacity to detect polygenic traits, and had a lower marker density. In this study, we performed genome-wide association study (GWAS) for SB resistance in hard winter wheat association mapping panel (HWWAMP) of 294 genotypes. The HWWAMP was evaluated for response to B. sorokiniana (isolate SD40), and a range of reactions was observed with 10 resistant, 38 moderately resistant, 120 moderately resistant- moderately susceptible, 111 moderately susceptible, and 15 susceptible genotypes. GWAS using 15,590 high-quality SNPs and 294 genotypes we identified six QTLs (p = <0.001) on chromosomes 2D, 3A, 4A, 4B, 5A, and 7B that collectively explained 30% of the total variation for SB resistance. Highly associated SNPs were identified for all six QTLs, QSb.sdsu-2D.1 (SNP: Kukri_c31121_1460, R2 = 4%), QSb.sdsu-3A.1 (SNP: Excalibur_c46082_440, R2 = 4%), QSb.sdsu-4A.1 (SNP: IWA8475, R2 = 5.5%), QSb.sdsu-4B.1 (SNP: Excalibur_rep_c79414_306, R2 = 4%), QSb.sdsu-5A.1 (SNP: Kukri_rep_c104877_2166, R2 = 6%), and QSb.sdsu-7B.1 (SNP: TA005844-0160, R2 = 6%). Our study not only validates three (2D, 5A, and 7B) genomic regions identified in previous studies but also provides highly associated SNP markers for marker assisted selection. In addition, we identified three novel QTLs (QSb.sdsu-3A.1, QSb.sdsu-4A.1, and QSb.sdsu-4B.1) for SB resistance in wheat. Gene annotation analysis of the candidate regions identified nine NBS-LRR and 38 other plant defense-related protein families across multiple QTLs, and these could be used for fine mapping and further characterization of SB resistance in wheat. Comparative analysis with barley indicated the SB resistance locus on wheat chromosomes 2D, 3A, 5A, and 7B identified in our study are syntenic to the previously identified SB resistance locus on chromosomes 2H, 3H, 5H, and 7H in barley. The 10 highly resistant genotypes and SNP markers identified in our study could be very useful resources for breeding of SB resistance in wheat.
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Affiliation(s)
- Girma T Ayana
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Shaukat Ali
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Jagdeep S Sidhu
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Jose L Gonzalez Hernandez
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Brent Turnipseed
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Sunish K Sehgal
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
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Roselló M, Royo C, Álvaro F, Villegas D, Nazco R, Soriano JM. Pasta-Making Quality QTLome From Mediterranean Durum Wheat Landraces. FRONTIERS IN PLANT SCIENCE 2018; 9:1512. [PMID: 30459781 PMCID: PMC6232839 DOI: 10.3389/fpls.2018.01512] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/26/2018] [Indexed: 05/22/2023]
Abstract
In order to identify genome regions related to pasta-making quality traits, association mapping (AM) was performed in a set of 165 durum wheat landraces from 21 Mediterranean countries. The collection was genotyped using 1149 DArT markers and 872 of them with a known genetic position were used for AM. The collection was grown in north-east Spain during 3 years. Results of ANOVA showed that trait variation for quality traits, except for grain protein content (GPC), was mainly explained by genetic effects. Landraces showed higher GPC than modern cultivars but lower gluten strength (GS). Modern and eastern landraces showed the highest yellow color index (YI). Balkan landraces showed the lowest test weight (TW). A total of 92 marker-trait associations were detected, 20 corresponding to GS, 21 to GPC, 21 to YI and 30 to TW. With the aim of detecting new genomic regions involved in grain quality, the position of the associations was compared with previously mapped QTL by a meta-QTL analysis. A total of 249 QTLs were projected onto the same map used for AM, identifying 45 meta-QTL (MQTL) regions and the remaining 15 QTLs as singletons. The position of known genes involved in grain quality was also included, and gene annotation within the most significant regions detected by AM was carried out using the wheat genome sequence.
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Iannucci A, Fragasso M, Beleggia R, Nigro F, Papa R. Evolution of the Crop Rhizosphere: Impact of Domestication on Root Exudates in Tetraploid Wheat ( Triticum turgidum L.). FRONTIERS IN PLANT SCIENCE 2017; 8:2124. [PMID: 29326736 PMCID: PMC5733359 DOI: 10.3389/fpls.2017.02124] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/29/2017] [Indexed: 05/23/2023]
Abstract
Domestication has induced major genetic changes in crop plants to satisfy human needs and as a consequence of adaptation to agroecosystems. This adaptation might have affected root exudate composition, which can influence the interactions in the rhizosphere. Here, using two different soil types (sand, soil), we provide an original example of the impact of domestication and crop evolution on root exudate composition through metabolite profiling of root exudates for a panel of 10 wheat genotypes that correspond to the key steps in domestication of tetraploid wheat (wild emmer, emmer, durum wheat). Our data show that soil type can dramatically affect the composition of root exudates in the rhizosphere. Moreover, the composition of the rhizosphere metabolites is associated with differences among the genotypes of the wheat domestication groups, as seen by the high heritability of some of the metabolites. Overall, we show that domestication and breeding have had major effects on root exudates in the rhizosphere, which suggests the adaptive nature of these changes.
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Affiliation(s)
- Anna Iannucci
- Centro di Ricerca per la Cerealicoltura e le Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'analisi dell'Economia Agraria (CREA-CI), Foggia, Italy
| | - Mariagiovanna Fragasso
- Centro di Ricerca per la Cerealicoltura e le Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'analisi dell'Economia Agraria (CREA-CI), Foggia, Italy
| | - Romina Beleggia
- Centro di Ricerca per la Cerealicoltura e le Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'analisi dell'Economia Agraria (CREA-CI), Foggia, Italy
| | - Franca Nigro
- Centro di Ricerca per la Cerealicoltura e le Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'analisi dell'Economia Agraria (CREA-CI), Foggia, Italy
| | - Roberto Papa
- Centro di Ricerca per la Cerealicoltura e le Colture Industriali, Consiglio per la Ricerca in Agricoltura e l'analisi dell'Economia Agraria (CREA-CI), Foggia, Italy
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, Ancona, Italy
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31
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Cell Membrane Stability and Association Mapping for Drought and Heat Tolerance in a Worldwide Wheat Collection. SUSTAINABILITY 2017. [DOI: 10.3390/su9091606] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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32
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Gahlaut V, Jaiswal V, Tyagi BS, Singh G, Sareen S, Balyan HS, Gupta PK. QTL mapping for nine drought-responsive agronomic traits in bread wheat under irrigated and rain-fed environments. PLoS One 2017; 12:e0182857. [PMID: 28793327 PMCID: PMC5550002 DOI: 10.1371/journal.pone.0182857] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 07/25/2017] [Indexed: 11/19/2022] Open
Abstract
In bread wheat, QTL interval mapping was conducted for nine important drought responsive agronomic traits. For this purpose, a doubled haploid (DH) mapping population derived from Kukri/Excalibur was grown over three years at four separate locations in India, both under irrigated and rain-fed environments. Single locus analysis using composite interval mapping (CIM) allowed detection of 98 QTL, which included 66 QTL for nine individual agronomic traits and 32 QTL, which affected drought sensitivity index (DSI) for the same nine traits. Two-locus analysis allowed detection of 19 main effect QTL (M-QTL) for four traits (days to anthesis, days to maturity, grain filling duration and thousand grain weight) and 19 pairs of epistatic QTL (E-QTL) for two traits (days to anthesis and thousand grain weight). Eight QTL were common in single locus analysis and two locus analysis. These QTL (identified both in single- and two-locus analysis) were distributed on 20 different chromosomes (except 4D). Important genomic regions on chromosomes 5A and 7A were also identified (5A carried QTL for seven traits and 7A carried QTL for six traits). Marker-assisted recurrent selection (MARS) involving pyramiding of important QTL reported in the present study, together with important QTL reported earlier, may be used for improvement of drought tolerance in wheat. In future, more closely linked markers for the QTL reported here may be developed through fine mapping, and the candidate genes may be identified and used for developing a better understanding of the genetic basis of drought tolerance in wheat.
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Affiliation(s)
- Vijay Gahlaut
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | - Vandana Jaiswal
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | - Bhudeva S. Tyagi
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Gyanendra Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Sindhu Sareen
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Harindra S. Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
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33
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Ovenden B, Milgate A, Wade LJ, Rebetzke GJ, Holland JB. Genome-Wide Associations for Water-Soluble Carbohydrate Concentration and Relative Maturity in Wheat Using SNP and DArT Marker Arrays. G3 (BETHESDA, MD.) 2017; 7:2821-2830. [PMID: 28655739 PMCID: PMC5555485 DOI: 10.1534/g3.117.039842] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/25/2017] [Indexed: 11/18/2022]
Abstract
Improving water-use efficiency by incorporating drought avoidance traits into new wheat varieties is an important objective for wheat breeding in water-limited environments. This study uses genome wide association studies (GWAS) to identify candidate loci for water-soluble carbohydrate accumulation-an important drought-avoidance characteristic in wheat. Phenotypes from a multi-environment trial with experiments differing in water availability and separate single nucleotide polymorphism (SNP) and diversity arrays technology (DArT) marker sets were used to perform the analyses. Significant associations for water-soluble carbohydrate accumulation were identified on chromosomes 1A, 1B, 1D, 2D, and 4A. Notably, these loci did not collocate with the major loci identified for relative maturity. Loci on chromosome 1D collocated with markers previously associated with the high molecular weight glutenin Glu-D1 locus. Genetic × environmental interactions impacted the results strongly, with significant associations for carbohydrate accumulation identified only in the water-deficit experiments. The markers associated with carbohydrate accumulation may be useful for marker-assisted selection of drought tolerance in wheat.
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Affiliation(s)
- Ben Ovenden
- New South Wales Department of Primary Industries, Yanco Agricultural Institute, New South Wales 2703, Australia
| | - Andrew Milgate
- New South Wales Department of Primary Industries, Wagga Wagga Agricultural Institute, New South Wales 2650, Australia
| | - Len J Wade
- Charles Sturt University, Graham Centre, Wagga Wagga, New South Wales 2678, Australia
| | - Greg J Rebetzke
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Canberra, Australian Capital Territory 2601, Australia
| | - James B Holland
- Plant Science Research Unit, United States Department of Agriculture-Agricultural Research Service, North Carolina State University, Raleigh, North Carolina 27695-7620
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina 27695-7620
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Wang DR, Han R, Wolfrum EJ, McCouch SR. The buffering capacity of stems: genetic architecture of nonstructural carbohydrates in cultivated Asian rice, Oryza sativa. THE NEW PHYTOLOGIST 2017; 215:658-671. [PMID: 28556941 PMCID: PMC5488208 DOI: 10.1111/nph.14614] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/28/2017] [Indexed: 05/13/2023]
Abstract
Harnessing stem carbohydrate dynamics in grasses offers an opportunity to help meet future demands for plant-based food, fiber and fuel production, but requires a greater understanding of the genetic controls that govern the synthesis, interconversion and transport of such energy reserves. We map out a blueprint of the genetic architecture of rice (Oryza sativa) stem nonstructural carbohydrates (NSC) at two critical developmental time-points using a subpopulation-specific genome-wide association approach on two diverse germplasm panels followed by quantitative trait loci (QTL) mapping in a biparental population. Overall, 26 QTL are identified; three are detected in multiple panels and are associated with starch-at-maturity, sucrose-at-maturity and NSC-at-heading. They tag OsHXK6 (rice hexokinase), ISA2 (rice isoamylase) and a tandem array of sugar transporters. This study provides the foundation for more in-depth molecular investigation to validate candidate genes underlying rice stem NSC and informs future comparative studies in other agronomically vital grass species.
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Affiliation(s)
- Diane R. Wang
- Section of Plant Breeding and GeneticsSchool of Integrated Plant SciencesCornell UniversityIthacaNY14853‐1901USA
| | - Rongkui Han
- Section of Plant Breeding and GeneticsSchool of Integrated Plant SciencesCornell UniversityIthacaNY14853‐1901USA
| | - Edward J. Wolfrum
- Integrated Biorefinery Research FacilityNational Renewable Energy LabGoldenCO80401USA
| | - Susan R. McCouch
- Section of Plant Breeding and GeneticsSchool of Integrated Plant SciencesCornell UniversityIthacaNY14853‐1901USA
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Soriano JM, Malosetti M, Roselló M, Sorrells ME, Royo C. Dissecting the old Mediterranean durum wheat genetic architecture for phenology, biomass and yield formation by association mapping and QTL meta-analysis. PLoS One 2017; 12:e0178290. [PMID: 28542488 PMCID: PMC5444813 DOI: 10.1371/journal.pone.0178290] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/10/2017] [Indexed: 12/01/2022] Open
Abstract
Association mapping was used to identify genome regions affecting yield formation, crop phenology and crop biomass in a collection of 172 durum wheat landraces representative of the genetic diversity of ancient local durum varieties from the Mediterranean Basin. The collection was genotyped with 1,149 DArT markers and phenotyped in Spanish northern and southern locations during three years. A total of 245 significant marker trait associations (MTAs) (P<0.01) were detected. Some of these associations confirmed previously identified quantitative trait loci (QTL) and/or candidate genes, and others are reported for the first time here. Eighty-six MTAs corresponded with yield and yield component traits, 70 to phenology and 89 to biomass production. Twelve genomic regions harbouring stable MTAs (significant in three or more environments) were identified, while five and two regions showed specific MTAs for northern and southern environments, respectively. Sixty per cent of MTAs were located on the B genome and 29% on the A genome. The marker wPt-9859 was detected in 12 MTAs, associated with six traits in four environments and the mean across years. To refine QTL positions, a meta-analysis was performed. A total of 477 unique QTLs were projected onto a durum wheat consensus map and were condensed to 71 meta-QTLs and left 13 QTLs as singletons. Sixty-one percent of QTLs explained less than 10% of the phenotypic variance confirming the high genetic complexity of the traits analysed.
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Affiliation(s)
- Jose Miguel Soriano
- Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), Lleida, Spain
| | - Marcos Malosetti
- Biometrics, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Martina Roselló
- Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), Lleida, Spain
| | - Mark Earl Sorrells
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States of America
| | - Conxita Royo
- Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), Lleida, Spain
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Mwadzingeni L, Shimelis H, Rees DJG, Tsilo TJ. Genome-wide association analysis of agronomic traits in wheat under drought-stressed and non-stressed conditions. PLoS One 2017; 12:e0171692. [PMID: 28234945 PMCID: PMC5325217 DOI: 10.1371/journal.pone.0171692] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 01/24/2017] [Indexed: 12/03/2022] Open
Abstract
This study determined the population structure and genome-wide marker-trait association of agronomic traits of wheat for drought-tolerance breeding. Ninety-three diverse bread wheat genotypes were genotyped using the Diversity Arrays Technology sequencing (DArTseq) protocol. The number of days-to-heading (DTH), number of days-to-maturity (DTM), plant height (PHT), spike length (SPL), number of kernels per spike (KPS), thousand kernel weight (TKW) and grain yield (GYLD), assessed under drought-stressed and non-stressed conditions, were considered for the study. Population structure analysis and genome-wide association mapping were undertaken based on 16,383 silico DArTs loci with < 10% missing data. The population evaluated was grouped into nine distinct genetic structures. Inter-chromosomal linkage disequilibrium showed the existence of linkage decay as physical distance increased. A total of 62 significant (P < 0.001) marker-trait associations (MTAs) were detected explaining more than 20% of the phenotypic variation observed under both drought-stressed and non-stressed conditions. Significant (P < 0.001) MTA event(s) were observed for DTH, PHT, SPL, SPS, and KPS; under both stressed and non-stressed conditions, while additional significant (P < 0.05) associations were observed for TKW, DTM and GYLD under non-stressed condition. The MTAs reported in this population could be useful to initiate marker-assisted selection (MAS) and targeted trait introgression of wheat under drought-stressed and non-stressed conditions, and for fine mapping and cloning of the underlying genes and QTL.
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Affiliation(s)
- Learnmore Mwadzingeni
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Agricultural Research Council-Small Grain Institute (ARC-SGI), Bethlehem, South Africa
| | - Hussein Shimelis
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - D. Jasper G. Rees
- Agricultural Research Council-Biotechnology Platform, Pretoria, South Africa
| | - Toi J. Tsilo
- Agricultural Research Council-Small Grain Institute (ARC-SGI), Bethlehem, South Africa
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Colasuonno P, Lozito ML, Marcotuli I, Nigro D, Giancaspro A, Mangini G, De Vita P, Mastrangelo AM, Pecchioni N, Houston K, Simeone R, Gadaleta A, Blanco A. The carotenoid biosynthetic and catabolic genes in wheat and their association with yellow pigments. BMC Genomics 2017; 18:122. [PMID: 28143400 PMCID: PMC5286776 DOI: 10.1186/s12864-016-3395-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 12/07/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND In plants carotenoids play an important role in the photosynthetic process and photo-oxidative protection, and are the substrate for the synthesis of abscisic acid and strigolactones. In addition to their protective role as antioxidants and precursors of vitamin A, in wheat carotenoids are important as they influence the colour (whiteness vs. yellowness) of the grain. Understanding the genetic basis of grain yellow pigments, and identifying associated markers provide the basis for improving wheat quality by molecular breeding. RESULTS Twenty-four candidate genes involved in the biosynthesis and catabolism of carotenoid compounds have been identified in wheat by comparative genomics. Single nucleotide polymorphisms (SNPs) found in the coding sequences of 19 candidate genes allowed their chromosomal location and accurate map position on two reference consensus maps to be determined. The genome-wide association study based on genotyping a tetraploid wheat collection with 81,587 gene-associated SNPs validated quantitative trait loci (QTLs) previously detected in biparental populations and discovered new QTLs for grain colour-related traits. Ten carotenoid genes mapped in chromosome regions underlying pigment content QTLs indicating possible functional relationships between candidate genes and the trait. CONCLUSIONS The availability of linked, candidate gene-based markers can facilitate breeding wheat cultivars with desirable levels of carotenoids. Identifying QTLs linked to carotenoid pigmentation can contribute to understanding genes underlying carotenoid accumulation in the wheat kernels. Together these outputs can be combined to exploit the genetic variability of colour-related traits for the nutritional and commercial improvement of wheat products.
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Affiliation(s)
- Pasqualina Colasuonno
- Department of Agricultural and Environmental Science, University of Bari 'Aldo Moro', Via G. Amendola 165/A, 70126, Bari, Italy
| | - Maria Luisa Lozito
- Department of Soil, Plant and Food Sciences, University of Bari 'Aldo Moro', Via G. Amendola 165/A, Bari, Italy
| | - Ilaria Marcotuli
- Department of Agricultural and Environmental Science, University of Bari 'Aldo Moro', Via G. Amendola 165/A, 70126, Bari, Italy
| | - Domenica Nigro
- Department of Soil, Plant and Food Sciences, University of Bari 'Aldo Moro', Via G. Amendola 165/A, Bari, Italy
| | - Angelica Giancaspro
- Department of Soil, Plant and Food Sciences, University of Bari 'Aldo Moro', Via G. Amendola 165/A, Bari, Italy
| | - Giacomo Mangini
- Department of Soil, Plant and Food Sciences, University of Bari 'Aldo Moro', Via G. Amendola 165/A, Bari, Italy
| | - Pasquale De Vita
- Council for Agricultural Research and Economics - Cereal Research Centre, 71122, Foggia, Italy
| | - Anna Maria Mastrangelo
- Council for Agricultural Research and Economics - Cereal Research Centre, 71122, Foggia, Italy
| | - Nicola Pecchioni
- Council for Agricultural Research and Economics - Cereal Research Centre, 71122, Foggia, Italy
| | - Kelly Houston
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland
| | - Rosanna Simeone
- Department of Soil, Plant and Food Sciences, University of Bari 'Aldo Moro', Via G. Amendola 165/A, Bari, Italy
| | - Agata Gadaleta
- Department of Agricultural and Environmental Science, University of Bari 'Aldo Moro', Via G. Amendola 165/A, 70126, Bari, Italy
| | - Antonio Blanco
- Department of Soil, Plant and Food Sciences, University of Bari 'Aldo Moro', Via G. Amendola 165/A, Bari, Italy.
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Genetic Diversity and Association Mapping for Agromorphological and Grain Quality Traits of a Structured Collection of Durum Wheat Landraces Including subsp. durum, turgidum and diccocon. PLoS One 2016; 11:e0166577. [PMID: 27846306 PMCID: PMC5113043 DOI: 10.1371/journal.pone.0166577] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/31/2016] [Indexed: 12/25/2022] Open
Abstract
Association mapping was performed for 18 agromorphological and grain quality traits in a set of 183 Spanish landraces, including subspecies durum, turgidum and dicoccon, genotyped with 749 DArT (Diversity Array Technology) markers. Large genetic and phenotypic variability was detected, being the level of diversity among the chromosomes and genomes heterogeneous, and sometimes complementary, among subspecies. Overall, 356 were monomorphic in at least one subspecies, mainly in dicoccon, and some of them coincidental between subspecies, especially between turgidum and dicoccon. Several of those fixed markers were associated to plant responses to environmental stresses or linked to genes subjected to selection during tetraploid wheat domestication process. A total of 85 stable MTAs (marker–trait associations) have been identified for the agromorphological and quality parameters, some of them common among subspecies and others subspecies-specific. For all the traits, we have found MTAs explaining more than 10% of the phenotypic variation in any of the three subspecies. The number of MTAs on the B genome exceeded that on the A genome in subsp. durum, equalled in turgidum and was below in dicoccon. The validation of several adaptive and quality trait MTAs by combining the association mapping with an analysis of the signature of selection, identifying the putative gene function of the marker, or by coincidences with previous reports, showed that our approach was successful for the detection of MTAs and the high potential of the collection to identify marker–trait associations. Novel MTAs not previously reported, some of them subspecies specific, have been described and provide new information about the genetic control of complex traits.
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Beleggia R, Rau D, Laidò G, Platani C, Nigro F, Fragasso M, De Vita P, Scossa F, Fernie AR, Nikoloski Z, Papa R. Evolutionary Metabolomics Reveals Domestication-Associated Changes in Tetraploid Wheat Kernels. Mol Biol Evol 2016; 33:1740-53. [PMID: 27189559 PMCID: PMC4915355 DOI: 10.1093/molbev/msw050] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Domestication and breeding have influenced the genetic structure of plant populations due to selection for adaptation from natural habitats to agro-ecosystems. Here, we investigate the effects of selection on the contents of 51 primary kernel metabolites and their relationships in three Triticum turgidum L. subspecies (i.e., wild emmer, emmer, durum wheat) that represent the major steps of tetraploid wheat domestication. We present a methodological pipeline to identify the signature of selection for molecular phenotypic traits (e.g., metabolites and transcripts). Following the approach, we show that a reduction in unsaturated fatty acids was associated with selection during domestication of emmer (primary domestication). We also show that changes in the amino acid content due to selection mark the domestication of durum wheat (secondary domestication). These effects were found to be partially independent of the associations that unsaturated fatty acids and amino acids have with other domestication-related kernel traits. Changes in contents of metabolites were also highlighted by alterations in the metabolic correlation networks, indicating wide metabolic restructuring due to domestication. Finally, evidence is provided that wild and exotic germplasm can have a relevant role for improvement of wheat quality and nutritional traits.
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Affiliation(s)
- Romina Beleggia
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per la Cerealicoltura (CREA-CER), Foggia, Italy
| | - Domenico Rau
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Giovanni Laidò
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per la Cerealicoltura (CREA-CER), Foggia, Italy
| | - Cristiano Platani
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per la Cerealicoltura (CREA-CER), Foggia, Italy Consiglio per la ricerca in agricoltura e l'analisi dell' economia agraria - Unità di Ricerca per l'Orticoltura (CREA-ORA), Monsampolo del Tronto (AP), Italy
| | - Franca Nigro
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per la Cerealicoltura (CREA-CER), Foggia, Italy
| | - Mariagiovanna Fragasso
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per la Cerealicoltura (CREA-CER), Foggia, Italy
| | - Pasquale De Vita
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per la Cerealicoltura (CREA-CER), Foggia, Italy
| | - Federico Scossa
- Consiglio per la ricerca in agricoltura e l'analisi dell' economia agraria, Centro di Ricerca per la Frutticoltura (CREA-FRU), Roma, Italy
| | - Alisdair R Fernie
- Central Metabolism Group, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Roberto Papa
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per la Cerealicoltura (CREA-CER), Foggia, Italy Dipartimento di Scienze Agrarie, Alimentari e Ambientali (D3A), Università Politecnica delle Marche, Ancona, Italy
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Association Mapping in Turkish Olive Cultivars Revealed Significant Markers Related to Some Important Agronomic Traits. Biochem Genet 2016; 54:506-533. [PMID: 27209034 DOI: 10.1007/s10528-016-9738-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/07/2016] [Indexed: 10/21/2022]
Abstract
Olive (Olea europaea L.) is one of the most important fruit trees especially in the Mediterranean countries due to high consumption of table olive and olive oil. In olive breeding, the phenotypic traits associated to fruit are the key factors that determine productivity. Association mapping has been used in some tree species and a lot of crop plant species, and here, we perform an initial effort to detect marker-trait associations in olive tree. In the current study, a total of 96 olive genotypes, including both oil and table olive genotypes from Turkish Olive GenBank Resources, were used to examine marker-trait associations. For olive genotyping, SNP, AFLP, and SSR marker data were selected from previously published study and association analysis was performed between these markers and 5 yield-related traits. Three different approaches were used to check for false-positive results in association tests, and association results obtained from these models were compared. Using the model utilizing both population structure and relative kinship, eleven associations were significant with FDR ≤ 0.05. The largest number of significant associations was detected for fruit weight and stone weight. Our results suggested that association mapping could be an effective approach for identifying marker-trait associations in olive genotypes, without the development of mapping populations. This study shows for the first time the use of association mapping for identifying molecular markers linked to important traits in olive tree.
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Lu D, Akanno EC, Crowley JJ, Schenkel F, Li H, De Pauw M, Moore SS, Wang Z, Li C, Stothard P, Plastow G, Miller SP, Basarab JA. Accuracy of genomic predictions for feed efficiency traits of beef cattle using 50K and imputed HD genotypes1. J Anim Sci 2016; 94:1342-53. [DOI: 10.2527/jas.2015-0126] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- D. Lu
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
- AgResearch, Invermay Agricultural Centre, Post Box 50034, Mosgiel 9053, New Zealand
| | - E. C. Akanno
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - J. J. Crowley
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
- Canadian Beef Breeds Council, Calgary, AB T2E 7H7, Canada
| | - F. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Sciences, University of Guelph, ON, Canada
| | - H. Li
- Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Sciences, University of Guelph, ON, Canada
| | - M. De Pauw
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - S. S. Moore
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Queensland, Australia
| | - Z. Wang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - C. Li
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
- Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Sciences, University of Guelph, ON, Canada
- Lacombe Research Centre, Agriculture and Agri-Food Canada, 6000 C & E Trail, Lacombe, AB, Canada
| | - P. Stothard
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - G. Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - S. P. Miller
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
- AgResearch, Invermay Agricultural Centre, Post Box 50034, Mosgiel 9053, New Zealand
- Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Sciences, University of Guelph, ON, Canada
| | - J. A. Basarab
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
- Lacombe Research Centre, Alberta Agriculture and Forestry, 6000 C & E Trail, Lacombe, AB, Canada
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Laidò G, Panio G, Marone D, Russo MA, Ficco DBM, Giovanniello V, Cattivelli L, Steffenson B, de Vita P, Mastrangelo AM. Identification of New Resistance Loci to African Stem Rust Race TTKSK in Tetraploid Wheats Based on Linkage and Genome-Wide Association Mapping. FRONTIERS IN PLANT SCIENCE 2015; 6:1033. [PMID: 26697025 PMCID: PMC4673868 DOI: 10.3389/fpls.2015.01033] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/06/2015] [Indexed: 05/22/2023]
Abstract
Stem rust, caused by Puccinia graminis Pers. f. sp. tritici Eriks. and E. Henn. (Pgt), is one of the most destructive diseases of wheat. Races of the pathogen in the "Ug99 lineage" are of international concern due to their virulence for widely used stem rust resistance genes and their spread throughout Africa. Disease resistant cultivars provide one of the best means for controlling stem rust. To identify quantitative trait loci (QTL) conferring resistance to African stem rust race TTKSK at the seedling stage, we evaluated an association mapping (AM) panel consisting of 230 tetraploid wheat accessions under greenhouse conditions. A high level of phenotypic variation was observed in response to race TTKSK in the AM panel, allowing for genome-wide association mapping of resistance QTL in wild, landrace, and cultivated tetraploid wheats. Thirty-five resistance QTL were identified on all chromosomes, and seventeen are of particular interest as identified by multiple associations. Many of the identified resistance loci were coincident with previously identified rust resistance genes; however, nine on chromosomes 1AL, 2AL, 4AL, 5BL, and 7BS may be novel. To validate AM results, a biparental population of 146 recombinant inbred lines was also considered, which derived from a cross between the resistant cultivar "Cirillo" and susceptible "Neodur." The stem rust resistance of Cirillo was conferred by a single gene on the distal region of chromosome arm 6AL in an interval map coincident with the resistance gene Sr13, and confirmed one of the resistance loci identified by AM. A search for candidate resistance genes was carried out in the regions where QTL were identified, and many of them corresponded to NBS-LRR genes and protein kinases with LRR domains. The results obtained in the present study are of great interest as a high level of genetic variability for resistance to race TTKSK was described in a germplasm panel comprising most of the tetraploid wheat sub-species.
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Affiliation(s)
- Giovanni Laidò
- Cereal Research Centre, Council for Agricultural Research and EconomicsFoggia, Italy
| | - Giosuè Panio
- Cereal Research Centre, Council for Agricultural Research and EconomicsFoggia, Italy
| | - Daniela Marone
- Cereal Research Centre, Council for Agricultural Research and EconomicsFoggia, Italy
| | - Maria A. Russo
- Cereal Research Centre, Council for Agricultural Research and EconomicsFoggia, Italy
| | - Donatella B. M. Ficco
- Cereal Research Centre, Council for Agricultural Research and EconomicsFoggia, Italy
| | | | - Luigi Cattivelli
- Cereal Research Centre, Council for Agricultural Research and EconomicsFoggia, Italy
- Genomics Research Centre, Council for Agricultural Research and EconomicsFiorenzuola d'Arda, Italy
| | - Brian Steffenson
- Department of Plant Pathology, University of Minnesota Twin CitiesMinneapolis, MN, USA
| | - Pasquale de Vita
- Cereal Research Centre, Council for Agricultural Research and EconomicsFoggia, Italy
| | - Anna M. Mastrangelo
- Cereal Research Centre, Council for Agricultural Research and EconomicsFoggia, Italy
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Gioia T, Nagel KA, Beleggia R, Fragasso M, Ficco DBM, Pieruschka R, De Vita P, Fiorani F, Papa R. Impact of domestication on the phenotypic architecture of durum wheat under contrasting nitrogen fertilization. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5519-30. [PMID: 26071535 DOI: 10.1093/jxb/erv289] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The process of domestication has led to dramatic morphological and physiological changes in crop species due to adaptation to cultivation and to the needs of farmers. To investigate the phenotypic architecture of shoot- and root-related traits and quantify the impact of primary and secondary domestication, we examined a collection of 36 wheat genotypes under optimal and nitrogen-starvation conditions. These represented three taxa that correspond to key steps in the recent evolution of tetraploid wheat (i.e. wild emmer, emmer, and durum wheat). Overall, nitrogen starvation reduced the shoot growth of all genotypes, while it induced the opposite effect on root traits, quantified using the automated phenotyping platform GROWSCREEN-Rhizo. We observed an overall increase in all of the shoot and root growth traits from wild emmer to durum wheat, while emmer was generally very similar to wild emmer but intermediate between these two subspecies. While the differences in phenotypic diversity due to the effects of primary domestication were not significant, the secondary domestication transition from emmer to durum wheat was marked by a large and significant decrease in the coefficient of additive genetic variation. In particular, this reduction was very strong under the optimal condition and less intense under nitrogen starvation. Moreover, although under the optimal condition both root and shoot traits showed significantly reduced diversity due to secondary domestication, under nitrogen starvation the reduced diversity was significant only for shoot traits. Overall, a considerable amount of phenotypic variation was observed in wild emmer and emmer, which could be exploited for the development of pre-breeding strategies.
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Affiliation(s)
- Tania Gioia
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria Centro di Ricerca per la Cerealicoltura (CRA-CER), S.S. 673 km 25,200, 71122, Foggia, Italy Institute of Biosciences and Geosciences (IBG-2): Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Kerstin A Nagel
- Institute of Biosciences and Geosciences (IBG-2): Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Romina Beleggia
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria Centro di Ricerca per la Cerealicoltura (CRA-CER), S.S. 673 km 25,200, 71122, Foggia, Italy
| | - Mariagiovanna Fragasso
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria Centro di Ricerca per la Cerealicoltura (CRA-CER), S.S. 673 km 25,200, 71122, Foggia, Italy
| | - Donatella Bianca Maria Ficco
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria Centro di Ricerca per la Cerealicoltura (CRA-CER), S.S. 673 km 25,200, 71122, Foggia, Italy
| | - Roland Pieruschka
- Institute of Biosciences and Geosciences (IBG-2): Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Pasquale De Vita
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria Centro di Ricerca per la Cerealicoltura (CRA-CER), S.S. 673 km 25,200, 71122, Foggia, Italy
| | - Fabio Fiorani
- Institute of Biosciences and Geosciences (IBG-2): Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Roberto Papa
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria Centro di Ricerca per la Cerealicoltura (CRA-CER), S.S. 673 km 25,200, 71122, Foggia, Italy Institute of Biosciences and Geosciences (IBG-2): Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy
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Hu X, Ren J, Ren X, Huang S, Sabiel SAI, Luo M, Nevo E, Fu C, Peng J, Sun D. Association of Agronomic Traits with SNP Markers in Durum Wheat (Triticum turgidum L. durum (Desf.)). PLoS One 2015; 10:e0130854. [PMID: 26110423 PMCID: PMC4482485 DOI: 10.1371/journal.pone.0130854] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/25/2015] [Indexed: 01/11/2023] Open
Abstract
Association mapping is a powerful approach to detect associations between traits of interest and genetic markers based on linkage disequilibrium (LD) in molecular plant breeding. In this study, 150 accessions of worldwide originated durum wheat germplasm (Triticum turgidum spp. durum) were genotyped using 1,366 SNP markers. The extent of LD on each chromosome was evaluated. Association of single nucleotide polymorphisms (SNP) markers with ten agronomic traits measured in four consecutive years was analyzed under a mix linear model (MLM). Two hundred and one significant association pairs were detected in the four years. Several markers were associated with one trait, and also some markers were associated with multiple traits. Some of the associated markers were in agreement with previous quantitative trait loci (QTL) analyses. The function and homology analyses of the corresponding ESTs of some SNP markers could explain many of the associations for plant height, length of main spike, number of spikelets on main spike, grain number per plant, and 1000-grain weight, etc. The SNP associations for the observed traits are generally clustered in specific chromosome regions of the wheat genome, mainly in 2A, 5A, 6A, 7A, 1B, and 6B chromosomes. This study demonstrates that association mapping can complement and enhance previous QTL analyses and provide additional information for marker-assisted selection.
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Affiliation(s)
- Xin Hu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan Hubei, 430070, China
| | - Jing Ren
- Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Institute of Biophysics, Dezhou University, Dezhou, Shandong, 253023, China
| | - Xifeng Ren
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan Hubei, 430070, China
| | - Sisi Huang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan Hubei, 430070, China
| | - Salih A. I. Sabiel
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan Hubei, 430070, China
| | - Mingcheng Luo
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, United States of America
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa, 31905, Israel
| | - Chunjie Fu
- Science and Technology Center, China National Seed Group Co., Ltd, Wuhan, Hubei, 430206, China
| | - Junhua Peng
- Science and Technology Center, China National Seed Group Co., Ltd, Wuhan, Hubei, 430206, China
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan Hubei, 430070, China
- Hubei Collaborative Innovation Center for Grain Industry, Jingzhou, Hubei, 434025, China
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Mohammadi M, Blake TK, Budde AD, Chao S, Hayes PM, Horsley RD, Obert DE, Ullrich SE, Smith KP. A genome-wide association study of malting quality across eight U.S. barley breeding programs. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:705-21. [PMID: 25666272 DOI: 10.1007/s00122-015-2465-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 01/17/2015] [Indexed: 05/18/2023]
Abstract
We report malt quality QTLs relevant to breeding with greater precision than previous mapping studies. The distribution of favorable alleles suggests strategies for marker-assisted breeding and germplasm exchange. This study leverages the breeding data of 1,862 barley breeding lines evaluated in 97 field trials for genome-wide association study of malting quality traits in barley. The mapping panel consisted of six-row and two-row advanced breeding lines from eight breeding populations established at six public breeding programs across the United States. A total of 4,976 grain samples were subjected to micro-malting analysis and mapping of nine quality traits was conducted with 3,072 SNP markers distributed throughout the genome. Association mapping was performed for individual breeding populations and for combined six-row and two-row populations. Only 16% of the QTL we report here had been detected in prior bi-parental mapping studies. Comparison of the analyses of the combined two-row and six-row panels identified only two QTL regions that were common to both. In total, 108 and 107 significant marker-trait associations were identified in all six-row and all two-row breeding programs, respectively. A total of 102 and 65 marker-trait associations were specific to individual six-row and two-row breeding programs, respectively indicating that most marker-trait associations were breeding population specific. Combining datasets from different breeding program resulted in both the loss of some QTL that were apparent in the analyses of individual programs and the discovery of new QTL not identified in individual programs. This suggests that simply increasing sample size by pooling samples with different breeding history does not necessarily increase the power to detect associations. The genetic architecture of malting quality and the distribution of favorable alleles suggest strategies for marker-assisted selection and germplasm exchange.
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Affiliation(s)
- Mohsen Mohammadi
- Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN, 55108-6026, USA
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Matschegewski C, Zetzsche H, Hasan Y, Leibeguth L, Briggs W, Ordon F, Uptmoor R. Genetic variation of temperature-regulated curd induction in cauliflower: elucidation of floral transition by genome-wide association mapping and gene expression analysis. FRONTIERS IN PLANT SCIENCE 2015; 6:720. [PMID: 26442034 PMCID: PMC4564693 DOI: 10.3389/fpls.2015.00720] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/27/2015] [Indexed: 05/09/2023]
Abstract
Cauliflower (Brassica oleracea var. botrytis) is a vernalization-responsive crop. High ambient temperatures delay harvest time. The elucidation of the genetic regulation of floral transition is highly interesting for a precise harvest scheduling and to ensure stable market supply. This study aims at genetic dissection of temperature-dependent curd induction in cauliflower by genome-wide association studies and gene expression analysis. To assess temperature-dependent curd induction, two greenhouse trials under distinct temperature regimes were conducted on a diversity panel consisting of 111 cauliflower commercial parent lines, genotyped with 14,385 SNPs. Broad phenotypic variation and high heritability (0.93) were observed for temperature-related curd induction within the cauliflower population. GWA mapping identified a total of 18 QTL localized on chromosomes O1, O2, O3, O4, O6, O8, and O9 for curding time under two distinct temperature regimes. Among those, several QTL are localized within regions of promising candidate flowering genes. Inferring population structure and genetic relatedness among the diversity set assigned three main genetic clusters. Linkage disequilibrium (LD) patterns estimated global LD extent of r(2) = 0.06 and a maximum physical distance of 400 kb for genetic linkage. Transcriptional profiling of flowering genes FLOWERING LOCUS C (BoFLC) and VERNALIZATION 2 (BoVRN2) was performed, showing increased expression levels of BoVRN2 in genotypes with faster curding. However, functional relevance of BoVRN2 and BoFLC2 could not consistently be supported, which probably suggests to act facultative and/or might evidence for BoVRN2/BoFLC-independent mechanisms in temperature-regulated floral transition in cauliflower. Genetic insights in temperature-regulated curd induction can underpin genetically informed phenology models and benefit molecular breeding strategies toward the development of thermo-tolerant cultivars.
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Affiliation(s)
- Claudia Matschegewski
- Chair of Agronomy, Faculty of Agriculture and Environmental Science, University of RostockRostock, Germany
- *Correspondence: Claudia Matschegewski, Chair of Agronomy, Faculty of Agriculture and Environmental Science, University of Rostock, Justus-von-Liebig-Weg 6, D-18059 Rostock, Germany,
| | - Holger Zetzsche
- Institute of Resistance Research and Stress Tolerance, Julius-Kuehn InstituteQuedlinburg, Germany
| | - Yaser Hasan
- Institute of Horticultural Production Systems, Leibniz Universität HannoverHannover, Germany
| | - Lena Leibeguth
- Chair of Agronomy, Faculty of Agriculture and Environmental Science, University of RostockRostock, Germany
| | | | - Frank Ordon
- Institute of Resistance Research and Stress Tolerance, Julius-Kuehn InstituteQuedlinburg, Germany
| | - Ralf Uptmoor
- Chair of Agronomy, Faculty of Agriculture and Environmental Science, University of RostockRostock, Germany
- Institute of Horticultural Production Systems, Leibniz Universität HannoverHannover, Germany
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Todorovska EG, Bozhanova V, Dechev D, Valkova N. Osmoregulation capacity in Bulgarian durum wheat. BIOTECHNOL BIOTEC EQ 2014; 28:786-797. [PMID: 26019562 PMCID: PMC4433794 DOI: 10.1080/13102818.2014.957054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 08/13/2014] [Indexed: 11/16/2022] Open
Abstract
The phenotypic variation in osmotic adjustment (OA) capacity of five Bulgarian winter durum wheat genotypes and their progenies was determined using a modified method based on the measurement of seedling growth suppression after three-day exposure to osmotic stress induced by 1 mol/L sucrose. The genetic parameters of the studied trait in a diallel crossing scheme, including the selected genotypes and the microsatellite polymorphism at 43 loci, were determined. The old Bulgarian cultivar Apulicum 233 and all hybrid combinations involving this genotype showed higher OA. In the heritability of osmoregulation ability, the non-additive gene effects (specific combining ability) strongly predominated over the additive ones and had a significant impact on the observed high heterosis effect. Distinct polymorphisms were identified between the studied genotypes. Cluster analysis of the phenotypic data obtained from a multiyear test under water-limited conditions and the molecular data, both based on Euclidean distance, showed similar grouping of the genotypes with specific separation of cultivar Apulicum 233 (high OA) in a single cluster. Principal component analysis revealed not only interrelationships between the important agronomic and morpho-physiological traits in Bulgarian durum wheat under water-limited conditions, but also presence of relations between them and some microsatellite loci located near or within known quantitative trait loci (QTLs) for these traits. Further studies based on segregating population between genotypes with contrasting levels of OA will allow mapping QTLs for phenotypic traits expressed under water deficit and isolation of genes that can be used as potential markers in marker-assisted selection for drought tolerance.
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